Job review #1473

Chain: A
1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96 101 106 111 116 121 126 131 136 141 146 151 156 161 166 171 176 181 186 191 196 201 206 211 216 221 226 231 236 241 246 251 256 261 266 271 276 281 286 291 296 301 306 311 316 321
QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRDOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Chain: B
1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96 101 106 111 116 121 126 131 136 141 146 151 156 161 166 171 176 181 186 191 196 201 206 211 216 221 226 231 236 241 246 251 256 261 266 271 276 281 286 291 296 301 306 311 316 321 326 331
DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Chain: C
22 27 32 37 42 47 52 57 62 67 72 77 82 87 92 97 102 107 112 117 122
SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQERRGH

Job #1473 review - http://mole.upol.cz/online/1473/

Generated on 2017-09-19 19:05:44 by service v2.3.29.2012.

9 tunnels click to expand / contract

  1. show | | profile | lining residues
    Tunnel 1 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 103 PHE C, 104 GLY C, 103 PHE C, 101 THR C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 103 PHE C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Physicochemical properties of lining side-chains

    Charge: 0 (0-0)
    Hydropathy: 1.5
    Hydrophobicity: 0.2
    Polarity: 1.5
    Mutability: 97

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 100 ILE C, 107 THR C, 2003 NA C
    4 100 ILE C, 103 PHE C, 104 GLY C
    5 100 ILE C, 103 PHE C, 107 THR C
    6 100 ILE C, 101 THR C, 103 PHE C
    7 101 THR C, 103 PHE C, 106 VAL C
    8 97 VAL C, 101 THR C, 103 PHE C
    9 33 THR C, 97 VAL C, 101 THR C
    10 33 THR C, 97 VAL C, 101 THR C

    layer with bottle neck

    layer with local minimum

  2. show | | profile | lining residues
    Tunnel 2 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 74 THR C, 103 PHE C, 100 ILE C, 103 PHE C, 104 GLY C, 107 THR C, 101 THR C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 103 PHE C, 107 THR C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Physicochemical properties of lining side-chains

    Charge: 0 (0-0)
    Hydropathy: 1.2
    Hydrophobicity: 0.08
    Polarity: 1.77
    Mutability: 97

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 74 THR C, 75 THR C, 100 ILE C
    3 74 THR C, 75 THR C, 2003 NA C
    4 74 THR C, 75 THR C, 103 PHE C
    5 74 THR C, 100 ILE C, 103 PHE C
    6 74 THR C, 75 THR C, 100 ILE C
    7 100 ILE C, 103 PHE C, 2003 NA C
    8 100 ILE C, 2003 NA C
    9 100 ILE C, 103 PHE C, 104 GLY C
    10 100 ILE C, 103 PHE C, 107 THR C
    11 100 ILE C, 101 THR C, 103 PHE C
    12 101 THR C, 103 PHE C, 106 VAL C
    13 97 VAL C, 101 THR C, 103 PHE C
    14 33 THR C, 97 VAL C, 101 THR C

    layer with bottle neck

    layer with local minimum

  3. show | | profile | lining residues
    Tunnel 3 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 74 THR C, 100 ILE C, 103 PHE C, 104 GLY C, 107 THR C, 101 THR C, 103 PHE C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 103 PHE C, 107 THR C, 101 THR C, 106 VAL C, 97 VAL C, 33 THR C

    Physicochemical properties of lining side-chains

    Charge: 0 (0-0)
    Hydropathy: 1.2
    Hydrophobicity: 0.1
    Polarity: 1.7
    Mutability: 97

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 74 THR C, 75 THR C, 100 ILE C
    3 74 THR C, 75 THR C, 100 ILE C
    4 74 THR C, 75 THR C, 100 ILE C
    5 100 ILE C, 103 PHE C, 2003 NA C
    6 103 PHE C, 104 GLY C, 2003 NA C
    7 103 PHE C, 2003 NA C
    8 103 PHE C, 107 THR C, 2003 NA C
    9 100 ILE C, 103 PHE C, 107 THR C
    10 100 ILE C, 101 THR C, 103 PHE C
    11 101 THR C, 103 PHE C, 106 VAL C
    12 97 VAL C, 101 THR C, 103 PHE C
    13 33 THR C, 97 VAL C, 101 THR C

    layer with bottle neck

    layer with local minimum

  4. show | | profile | lining residues
    Tunnel 4 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 100 ILE C, 104 GLY C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C

    Physicochemical properties of lining side-chains

    Charge: 0 (0-0)
    Hydropathy: -0.6
    Hydrophobicity: -0.29
    Polarity: 9.67
    Mutability: 98

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 100 ILE C, 104 GLY C, 2003 NA C
    4 104 GLY C, 2003 NA C
    5 104 GLY C, 107 THR C, 2003 NA C
    6 107 THR C, 2003 NA C
    7 107 THR C
    8 107 THR C, 2003 NA C
    9 107 THR C
    10 107 THR C, 2003 NA C
    11 107 THR C
    12 107 THR C, 111 ALA C
    13 111 ALA C
    14 111 ALA C, 115 VAL C
    15 115 VAL C
    16 115 VAL C, 119 GLN C
    17 119 GLN C
    18 115 VAL C, 119 GLN C
    19 119 GLN C
    20 119 GLN C, 124 HIS C
    21 124 HIS C
    22 119 GLN C, 124 HIS C
    23 124 HIS C
    24 119 GLN C, 124 HIS C
    25 124 HIS C

    layer with bottle neck

    layer with local minimum

  5. show | | profile | lining residues
    Tunnel 5 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 100 ILE C, 104 GLY C, 107 THR C, 111 ALA C, 108 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 123 GLY C, 122 ARG C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C,

    Physicochemical properties of lining side-chains

    Charge: 0 (0-0)
    Hydropathy: -0.7
    Hydrophobicity: -0.33
    Polarity: 10.96
    Mutability: 98

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 100 ILE C, 104 GLY C, 2003 NA C
    4 104 GLY C, 2003 NA C
    5 104 GLY C, 107 THR C, 2003 NA C
    6 107 THR C, 2003 NA C
    7 107 THR C
    8 107 THR C, 2003 NA C
    9 107 THR C
    10 107 THR C, 2003 NA C
    11 107 THR C
    12 107 THR C, 111 ALA C
    13 108 ALA C, 111 ALA C
    14 111 ALA C
    15 111 ALA C, 115 VAL C
    16 115 VAL C
    17 115 VAL C, 119 GLN C
    18 119 GLN C
    19 115 VAL C, 119 GLN C
    20 119 GLN C
    21 119 GLN C, 124 HIS C
    22 124 HIS C
    23 119 GLN C, 124 HIS C
    24 124 HIS C
    25 119 GLN C, 124 HIS C
    26 124 HIS C
    27 123 GLY C, 124 HIS C
    28 122 ARG C, 123 GLY C, 124 HIS C
    29 122 ARG C, 124 HIS C

    layer with bottle neck

    layer with local minimum

  6. show | | profile | lining residues
    Tunnel 6 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 104 GLY C, 107 THR C, 111 ALA C, 108 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 122 ARG C, 116 GLY C, 120 GLU C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 122 ARG C, 120 GLU C

    Physicochemical properties of lining side-chains

    Charge: 0 (1-1)
    Hydropathy: -1.3
    Hydrophobicity: -0.37
    Polarity: 16.74
    Mutability: 94

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 104 GLY C, 2003 NA C
    4 104 GLY C, 107 THR C, 2003 NA C
    5 107 THR C, 2003 NA C
    6 107 THR C
    7 107 THR C, 2003 NA C
    8 107 THR C
    9 107 THR C, 2003 NA C
    10 107 THR C
    11 107 THR C, 111 ALA C
    12 108 ALA C, 111 ALA C
    13 111 ALA C
    14 111 ALA C, 115 VAL C
    15 115 VAL C
    16 115 VAL C, 119 GLN C
    17 119 GLN C
    18 115 VAL C, 119 GLN C
    19 119 GLN C
    20 119 GLN C, 124 HIS C
    21 124 HIS C
    22 119 GLN C, 124 HIS C
    23 119 GLN C, 122 ARG C, 124 HIS C
    24 116 GLY C, 119 GLN C, 122 ARG C
    25 116 GLY C, 119 GLN C, 120 GLU C
    26 116 GLY C, 120 GLU C, 122 ARG C
    27 120 GLU C, 122 ARG C, 124 HIS C

    layer with bottle neck

    layer with local minimum

  7. show | | profile | lining residues
    Tunnel 7 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 100 ILE C, 104 GLY C, 107 THR C, 111 ALA C, 108 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 123 GLY C, 122 ARG C, 120 GLU C, 122 ARG C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 120 GLU C, 122 ARG C

    Physicochemical properties of lining side-chains

    Charge: 0 (1-1)
    Hydropathy: -0.9
    Hydrophobicity: -0.36
    Polarity: 13.65
    Mutability: 94

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 100 ILE C, 104 GLY C, 2003 NA C
    4 104 GLY C, 2003 NA C
    5 104 GLY C, 107 THR C, 2003 NA C
    6 107 THR C, 2003 NA C
    7 107 THR C
    8 107 THR C, 2003 NA C
    9 107 THR C
    10 107 THR C, 2003 NA C
    11 107 THR C
    12 107 THR C, 111 ALA C
    13 108 ALA C, 111 ALA C
    14 111 ALA C
    15 111 ALA C, 115 VAL C
    16 115 VAL C
    17 115 VAL C, 119 GLN C
    18 119 GLN C
    19 115 VAL C, 119 GLN C
    20 119 GLN C
    21 119 GLN C, 124 HIS C
    22 124 HIS C
    23 119 GLN C, 124 HIS C
    24 124 HIS C
    25 119 GLN C, 124 HIS C
    26 124 HIS C
    27 119 GLN C, 124 HIS C
    28 124 HIS C
    29 123 GLY C, 124 HIS C
    30 122 ARG C, 123 GLY C, 124 HIS C
    31 122 ARG C, 124 HIS C
    32 120 GLU C, 122 ARG C, 124 HIS C

    layer with bottle neck

    layer with local minimum

  8. show | | profile | lining residues
    Tunnel 8 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 104 GLY C, 107 THR C, 111 ALA C, 108 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 122 ARG C, 116 GLY C, 118 GLU C, 120 GLU C, 121 ARG C, 117 ARG C, 26 TRP C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 122 ARG C, 118 GLU C, 120 GLU C, 121 ARG C, 117 ARG C, 26 TRP C

    Physicochemical properties of lining side-chains

    Charge: 1 (3-2)
    Hydropathy: -2
    Hydrophobicity: -0.5
    Polarity: 24.94
    Mutability: 86

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 104 GLY C, 2003 NA C
    4 104 GLY C, 107 THR C, 2003 NA C
    5 107 THR C, 2003 NA C
    6 107 THR C
    7 107 THR C, 2003 NA C
    8 107 THR C
    9 107 THR C, 2003 NA C
    10 107 THR C
    11 107 THR C, 111 ALA C
    12 108 ALA C, 111 ALA C
    13 111 ALA C
    14 111 ALA C, 115 VAL C
    15 115 VAL C
    16 115 VAL C, 119 GLN C
    17 119 GLN C
    18 115 VAL C, 119 GLN C
    19 119 GLN C
    20 119 GLN C, 124 HIS C
    21 124 HIS C
    22 119 GLN C, 124 HIS C
    23 119 GLN C, 122 ARG C, 124 HIS C
    24 119 GLN C, 122 ARG C
    25 116 GLY C, 119 GLN C, 122 ARG C
    26 116 GLY C, 118 GLU C, 122 ARG C
    27 116 GLY C, 120 GLU C, 122 ARG C
    28 116 GLY C, 118 GLU C, 120 GLU C
    29 118 GLU C, 120 GLU C, 122 ARG C
    30 118 GLU C, 120 GLU C, 121 ARG C
    31 118 GLU C, 120 GLU C, 121 ARG C
    32 117 ARG C, 118 GLU C, 120 GLU C
    33 117 ARG C, 118 GLU C, 121 ARG C
    34 26 TRP C, 117 ARG C, 118 GLU C

    layer with bottle neck

    layer with local minimum

  9. show | | profile | lining residues
    Tunnel 9 profile

    Unique lining residues set - all

    75 THR C, 100 ILE C, 2003 NA C, 104 GLY C, 107 THR C, 111 ALA C, 108 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 123 GLY C, 122 ARG C, 120 GLU C, 122 ARG C, 121 ARG C, 117 ARG C, 118 GLU C, 26 TRP C

    Unique lining residues set - sidechains

    75 THR C, 100 ILE C, 2003 NA C, 107 THR C, 111 ALA C, 115 VAL C, 119 GLN C, 124 HIS C, 120 GLU C, 122 ARG C, 121 ARG C, 117 ARG C, 118 GLU C, 26 TRP C

    Physicochemical properties of lining side-chains

    Charge: 1 (3-2)
    Hydropathy: -1.6
    Hydrophobicity: -0.4
    Polarity: 21.68
    Mutability: 86

    Lining residues

    show all | hide all

    # Res Btn Dist Hpa Hpb Pol Mut
    1 75 THR C, 100 ILE C, 2003 NA C
    2 100 ILE C, 2003 NA C
    3 104 GLY C, 2003 NA C
    4 104 GLY C, 107 THR C, 2003 NA C
    5 107 THR C, 2003 NA C
    6 107 THR C
    7 107 THR C, 2003 NA C
    8 107 THR C
    9 107 THR C, 2003 NA C
    10 107 THR C
    11 107 THR C, 111 ALA C
    12 108 ALA C, 111 ALA C
    13 111 ALA C
    14 111 ALA C, 115 VAL C
    15 115 VAL C
    16 115 VAL C, 119 GLN C
    17 119 GLN C
    18 115 VAL C, 119 GLN C
    19 119 GLN C
    20 119 GLN C, 124 HIS C
    21 124 HIS C
    22 119 GLN C, 124 HIS C
    23 124 HIS C
    24 119 GLN C, 124 HIS C
    25 124 HIS C
    26 123 GLY C, 124 HIS C
    27 122 ARG C, 123 GLY C, 124 HIS C
    28 122 ARG C, 124 HIS C
    29 120 GLU C, 122 ARG C, 124 HIS C
    30 120 GLU C, 122 ARG C
    31 120 GLU C, 121 ARG C, 122 ARG C
    32 120 GLU C, 121 ARG C
    33 117 ARG C, 120 GLU C, 121 ARG C
    34 117 ARG C, 121 ARG C
    35 117 ARG C, 118 GLU C, 121 ARG C
    36 26 TRP C, 117 ARG C, 118 GLU C

    layer with bottle neck

    layer with local minimum

show all | hide all

You can download all tunnels as PyMol script, PDB file or print the report.

38 cavities click to expand / contract

  1. (volume ~ 17813 Å3)
  2. (volume ~ 7425 Å3)
  3. (volume ~ 3896 Å3)
  4. (volume ~ 3896 Å3)
  5. (volume ~ 3896 Å3)
  6. (volume ~ 3896 Å3)
  7. (volume ~ 2964 Å3)
  8. (volume ~ 2964 Å3)
  9. (volume ~ 2964 Å3)
  10. (volume ~ 2964 Å3)
  11. (volume ~ 1466 Å3)
  12. (volume ~ 1466 Å3)
  13. (volume ~ 1466 Å3)
  14. (volume ~ 1466 Å3)
  15. (volume ~ 926 Å3)
  16. (volume ~ 926 Å3)
  17. (volume ~ 926 Å3)
  18. (volume ~ 926 Å3)
  19. (volume ~ 913 Å3)
  20. (volume ~ 913 Å3)
  21. (volume ~ 913 Å3)
  22. (volume ~ 913 Å3)
  23. (volume ~ 482 Å3)
  24. (volume ~ 482 Å3)
  25. (volume ~ 482 Å3)
  26. (volume ~ 482 Å3)
  27. (volume ~ 468 Å3)
  28. (volume ~ 468 Å3)
  29. (volume ~ 468 Å3)
  30. (volume ~ 468 Å3)
  31. (volume ~ 152 Å3)
  32. (volume ~ 152 Å3)
  33. (volume ~ 152 Å3)
  34. (volume ~ 152 Å3)
  35. (volume ~ 143 Å3)
  36. (volume ~ 143 Å3)
  37. (volume ~ 143 Å3)
  38. (volume ~ 143 Å3)
show all | hide all

Features click to expand / contract

The surface is affected by the Probe Radius parameter.

Settings click to expand / contract

Structure: 1k4d (structure summary on pdb.org)
Unit: 1
Identify tunnels starting from multiple cavities. This can provide a good initial insight into the tunnel structure of the protein.
: clear
Example: GLU 308, THR 309
The starting point is defined as a center of mass of selected residues. You can choose residues using by the sequence inspector below the Jmol window. In case you analyze an enzyme structure, MOLEOnline offers an active site residues (from the Catalytic Site Atlas, if available) as the starting point.
Active sites from CSA:

No sites found.

Ignoring coordinates with HETATM records for non-polymer or other “non-standard” chemical coordinates, such as atoms presented in HET groups (ligands, prosthetic groups) in PDB format. Reminder: water molecules (WAT, HOH, SOL) are ignored everytime in MOLEonline 2.0!

Advanced Settings click to expand / contract

:
Example: A GLU 308, B THR 309.
List of residues to be ignored prior computation of channel.
Starting point [X,Y,Z]: clear
Specify starting point as an X, Y, Z coordinates (as decimal numbers in Å).
:
Radius used for construction of molecular surface.
:
Lower bound of the tunnel radius.
:
Determines the density of tunnel exits on the molecular surface.
:
Better starting points are localized within the defined radius from the original starting point.
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Tunnels with bottleneck bellow this radius will be removed.
:
Used to remove tunnels based on their percentage similarity.

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