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ENV_HV1Y2_326_479

Envelope glycoprotein gp160 [HIV-1 env protein family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ENV_HV1Y2):R: CD4-binding loop (362, 363, 365, 366)
108, 111, 206, 251:253, 370:372, 377, 379, 408, 411:417, 422, 459:463
108, 111, 206, 251:253, 362, 363, 365, 366, 370:372, 377, 379, 408, 411:417, 422, 459:463

Full PDB list

1g9n, 1rzk, 1yyl, 1yym, 2i5y, 2i60, 2qad, 3hi1, 3tgq, 4dvr, 4jzw, 4jzz, 4k0a, 4ka2, 4laj, 4rwy, 5ukr (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
0
8
W
1
1
1
F
2
0
6
V
2
5
1
T
2
5
3
G
3
6
2
D
3
6
3
E
3
6
5
I
3
6
6
S
3
7
0
F
3
7
1
N
3
7
2
F
3
7
7
Y
3
7
9
K
4
0
8
I
4
1
1
N
4
1
2
M
4
1
3
W
4
1
4
Q
4
1
5
E
4
1
6
V
4
1
7
G
4
6
0
D
4
6
1
M
4
6
2
R
4
6
3
[1]1yyl.g GSbif27 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yyl.p Sbif23 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yym.g GSF21 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2i5y.g dprTbif31 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2i60.g dprTF25 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3tgq.c none . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dvr.g 0ly23 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4jzw.g dprTu2x33 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k0a.a dprT1op32 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ka2.a dprTu3x33 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rwy.a R11 . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3hi1.g S-Y-AVFY53 . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3hi1.j SHY-AVFY63 . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5ukr.g V,Y19 . . - . . . . . . . . . . . . . . . - - - - . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

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PDB.ch
A1
I
1
0
8
W
1
1
1
F
2
0
6
V
2
5
1
S
2
5
2
T
2
5
3
G
3
6
2
D
3
6
3
E
3
6
5
I
3
6
6
S
3
7
0
F
3
7
1
N
3
7
2
F
3
7
7
Y
3
7
9
K
4
0
8
I
4
1
1
N
4
1
2
M
4
1
3
W
4
1
4
Q
4
1
5
E
4
1
6
V
4
1
7
Y
4
2
2
G
4
5
9
G
4
6
0
D
4
6
1
M
4
6
2
R
4
6
3
[1]1yyl.g . . . . . . . . . . . . . . . . * . * * . . . . . . . . *
[1]1yyl.p . . . . . . . . . . . . . . . . * . * * * . . . . . . . *
[1]1yym.g . * . . . . . . . . . . . . . . * . * * * . . . . . . . .
[1]2i5y.g . . . . . . . . . . . . . . . . * . * * . . . . . . . . *
[1]2i60.g . * . . . . . . . . . . . . . . * . * * * . . . . . . . *
[1]3tgq.c . . . . . . . . . . . . . . . . * . * * * . . . . . . . .
[1]4dvr.g . . . . . . . . . . . . . . . . * * * * * . . . . . . . .
[1]4jzw.g . * . . . . . . . . . . . . . . * . * * * . . . . . . . .
[1]4k0a.a . . . . . . . . . . . . . . . . * . * * * . . . . . . . .
[1]4ka2.a . * . . . . . . . . . . . . . . * . * * * . . . . . . . .
[1]4rwy.a . * . . . . . . . . . . . . . . . * * * * . . . . . . . .
[2]3hi1.g . . . . . . . . . . . . . . . . . . . . . . . . . . . . *
[2]3hi1.j . . . . . . . . . . . . . . . . . . . . . . . . . . . . *
[2]5ukr.g . . - . . . . * * . . . . * . . . . . - - - - - . . . . *

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1yyl.g:GSbif
1yyl.p:Sbif
1yym.g:GSF
2i5y.g:dprTbif
2i60.g:dprTF
3tgq.c is apo
4dvr.g:0ly
4jzw.g:dprTu2x
4k0a.a:dprT1op
4ka2.a:dprTu3x
4rwy.a:R
3hi1.g:S-Y-AVFY
3hi1.j:SHY-AVFY
5ukr.g:V,Y
[1] 1yyl.g
0
0 0 0.1 0.1 - 0.4 0.2 0.1 0.3 0.7 11 11 1.5
[1] 1yyl.p 0
0
0 0 0 - 0.4 0.1 0.1 0.2 0.7 12 11 1.9
[1] 1yym.g 0.2 0.2
0
0.3 0 - 0.4 0.1 0.1 0.2 0.5 12 11 1.8
[1] 2i5y.g 0 0 0
0
0 - 0.3 0.1 0.3 0.2 0.9 11 11 1.5
[1] 2i60.g 0.1 0.2 0 0.3
0
- 0.4 0.1 0.1 0 0.9 11 11 1.8
[1] 3tgq.c 0.2 0.3 0.1 0.4 0.1
-
0.2 0.2 0.1 0.1 0 11 11 2.0
[1] 4dvr.g 0.2 0.3 0.1 0.2 0 -
0
0.2 0.3 0.2 0.3 11 11 1.8
[1] 4jzw.g 0 0.2 0 0.1 0 - 0.1
0
0 0 0 11 11 1.5
[1] 4k0a.a 0.1 0.2 0 0.1 0 - 0.2 0.1
0
0 0 12 11 1.3
[1] 4ka2.a 0 0.3 0 0.1 0 - 0.1 0 0
0
0 11 11 1.3
[1] 4rwy.a 0.3 0.2 0.1 0.2 0.1 - 0 0.2 0.2 0.2
0
12 11 1.4
[2] 3hi1.g 0.3 0 0.1 0.2 0.2 - 0.3 0.4 0.5 0.7 0.9
0
0 0
[2] 3hi1.j 0.1 0 0.1 0.2 0.2 - 0.2 0.4 0.5 0.7 0.9 0
0
0
[2] 5ukr.g 0.8 0.8 0.3 0.7 0.3 - 1.7 2.5 2.2 2.8 0.7 1.9 3.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1yyl.g
1yyl.p
1yym.g
2i5y.g
2i60.g
3tgq.c
4dvr.g
4jzw.g
4k0a.a
4ka2.a
4rwy.a
3hi1.g
3hi1.j
5ukr.g
[1] 1yyl.g
0
.04 .10 .04 .11 .12 .12 .15 .13 .14 .19 .42 .42 .53
[1] 1yyl.p .04
0
.07 .05 .10 .14 .11 .14 .11 .15 .18 .44 .44 .56
[1] 1yym.g .10 .07
0
.11 .04 .11 .10 .10 .09 .11 .13 .47 .47 .58
[1] 2i5y.g .04 .05 .11
0
.11 .12 .13 .15 .13 .14 .19 .41 .41 .54
[1] 2i60.g .11 .10 .04 .11
0
.11 .12 .10 .10 .11 .15 .43 .43 .55
[1] 3tgq.c .12 .14 .11 .12 .11
0
.08 .08 .05 .05 .14 .49 .49 .59
[1] 4dvr.g .12 .11 .10 .13 .12 .08
0
.07 .08 .07 .13 .49 .49 .60
[1] 4jzw.g .15 .14 .10 .15 .10 .08 .07
0
.04 .03 .12 .48 .48 .59
[1] 4k0a.a .13 .11 .09 .13 .10 .05 .08 .04
0
.04 .15 .49 .48 .59
[1] 4ka2.a .14 .15 .11 .14 .11 .05 .07 .03 .04
0
.13 .48 .48 .58
[1] 4rwy.a .19 .18 .13 .19 .15 .14 .13 .12 .15 .13
0
.49 .49 .56
[2] 3hi1.g .42 .44 .47 .41 .43 .49 .49 .48 .49 .48 .49
0
0 .16
[2] 3hi1.j .42 .44 .47 .41 .43 .49 .49 .48 .48 .48 .49 0
0
.16
[2] 5ukr.g .53 .56 .58 .54 .55 .59 .60 .59 .59 .58 .56 .16 .16
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1yyl.g
1yyl.p
1yym.g
2i5y.g
2i60.g
3tgq.c
4dvr.g
4jzw.g
4k0a.a
4ka2.a
4rwy.a
3hi1.g
3hi1.j
5ukr.g
[1] 1yyl.g
0
0.3 0.3 0.2 0.3 0.8 0.8 0.7 0.7 0.7 1.1 9.8 9.4 4.0
[1] 1yyl.p 0.3
0
0.3 0.3 0.4 0.7 0.7 0.7 0.7 0.6 1.0 9.8 9.4 4.0
[1] 1yym.g 0.3 0.3
0
0.4 0.2 0.6 0.7 0.6 0.6 0.6 1.0 9.9 9.4 4.0
[1] 2i5y.g 0.2 0.3 0.4
0
0.3 0.8 0.7 0.7 0.6 0.7 1.1 9.8 9.4 4.0
[1] 2i60.g 0.3 0.4 0.2 0.3
0
0.7 0.7 0.6 0.6 0.6 1.0 9.9 9.4 4.0
[1] 3tgq.c 0.8 0.7 0.6 0.8 0.7
0
0.4 0.4 0.4 0.4 0.9 10 9.5 4.1
[1] 4dvr.g 0.8 0.7 0.7 0.7 0.7 0.4
0
0.4 0.4 0.4 0.9 9.9 9.4 4.1
[1] 4jzw.g 0.7 0.7 0.6 0.7 0.6 0.4 0.4
0
0.2 0.1 0.8 9.8 9.4 4.0
[1] 4k0a.a 0.7 0.7 0.6 0.6 0.6 0.4 0.4 0.2
0
0.2 0.8 9.8 9.3 4.1
[1] 4ka2.a 0.7 0.6 0.6 0.7 0.6 0.4 0.4 0.1 0.2
0
0.8 9.8 9.4 4.0
[1] 4rwy.a 1.1 1.0 1.0 1.1 1.0 0.9 0.9 0.8 0.8 0.8
0
9.3 8.9 3.8
[2] 3hi1.g 9.8 9.8 9.9 9.8 9.9 10 9.9 9.8 9.8 9.8 9.3
0
1.2 1.7
[2] 3hi1.j 9.4 9.4 9.4 9.4 9.4 9.5 9.4 9.4 9.3 9.4 8.9 1.2
0
1.6
[2] 5ukr.g 4.0 4.0 4.0 4.0 4.0 4.1 4.1 4.0 4.1 4.0 3.8 1.7 1.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1yyl.g
1yyl.p
1yym.g
2i5y.g
2i60.g
3tgq.c
4dvr.g
4jzw.g
4k0a.a
4ka2.a
4rwy.a
3hi1.g
3hi1.j
5ukr.g
[1] 1yyl.g
0
0.4 0.4 0.3 0.4 1.0 0.9 1.0 1.0 1.0 1.3 10 10 4.0
[1] 1yyl.p 0.4
0
0.5 0.4 0.5 1.0 0.9 1.0 1.0 1.0 1.3 10 10 4.0
[1] 1yym.g 0.4 0.5
0
0.4 0.2 0.9 0.8 0.9 0.9 0.9 1.2 10 10 4.0
[1] 2i5y.g 0.3 0.4 0.4
0
0.4 1.0 0.9 0.9 0.9 0.9 1.3 10 10 4.0
[1] 2i60.g 0.4 0.5 0.2 0.4
0
0.9 0.8 0.9 0.9 0.9 1.2 10 10 4.0
[1] 3tgq.c 1.0 1.0 0.9 1.0 0.9
0
0.9 0.8 0.8 0.8 1.1 10 10 4.0
[1] 4dvr.g 0.9 0.9 0.8 0.9 0.8 0.9
0
0.8 0.8 0.8 1.2 10 10 4.0
[1] 4jzw.g 1.0 1.0 0.9 0.9 0.9 0.8 0.8
0
0.3 0.2 0.9 10 10 4.0
[1] 4k0a.a 1.0 1.0 0.9 0.9 0.9 0.8 0.8 0.3
0
0.3 0.9 10 10 4.0
[1] 4ka2.a 1.0 1.0 0.9 0.9 0.9 0.8 0.8 0.2 0.3
0
0.9 10 10 4.0
[1] 4rwy.a 1.3 1.3 1.2 1.3 1.2 1.1 1.2 0.9 0.9 0.9
0
9.8 9.6 3.7
[2] 3hi1.g 10 10 10 10 10 10 10 10 10 10 9.8
0
1.8 2.5
[2] 3hi1.j 10 10 10 10 10 10 10 10 10 10 9.6 1.8
0
2.5
[2] 5ukr.g 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 3.7 2.5 2.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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