eF-site ID 6d2p-CHL
PDB Code 6d2p
Chain C, H, L

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Title Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.6 A
Classification IMMUNE SYSTEM
Compound Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
Source (6D2P)
Sequence C:  DTITLPCRPAPPPHCSSNITGLILTRQGGYSNANTVIFRP
SGGDWRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSEDW
RDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIA
SKLREQYGAKTIIFKPSSGGDPEFVNHSFNCGGEFFYCAS
TQLFASTWF
H:  QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQA
PGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAY
MELSRLRSDDTAVYYCARSLGRDWFDPWGQGTLVTVSSAS
TKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP
SNTKVDKKVEPKS
L:  SALTQPASVSGSPGQSITISCTGTSSDVGSNLVSWYQQHP
GKAPKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQA
EDEADYYCCSYAGSVVFGGGTKLTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVE
TTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGS
TVEKTVAPTE
Description (1)  VRC01cHuGL2 Fab heavy chain, VRC01c-HuGL2 Fab light chain, Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8


Functional site

1) chain C
residue 14
type
ligand
sequence H
description binding site for residue GOL C 201
source : AC1

2) chain C
residue 16
type
ligand
sequence S
description binding site for residue GOL C 201
source : AC1

3) chain C
residue 17
type
ligand
sequence S
description binding site for residue GOL C 201
source : AC1

4) chain C
residue 65
type
ligand
sequence N
description binding site for residue GOL C 201
source : AC1

5) chain C
residue 18
type
ligand
sequence N
description binding site for residue GOL C 202
source : AC2

6) chain C
residue 96
type
ligand
sequence E
description binding site for residue GOL C 202
source : AC2

7) chain C
residue 137
type
ligand
sequence S
description binding site for residue GOL C 203
source : AC3

8) chain C
residue 145
type
ligand
sequence V
description binding site for residue GOL C 203
source : AC3

9) chain C
residue 146
type
ligand
sequence N
description binding site for residue GOL C 203
source : AC3

10) chain C
residue 159
type
ligand
sequence A
description binding site for residue GOL C 203
source : AC3

11) chain C
residue 160
type
ligand
sequence S
description binding site for residue GOL C 203
source : AC3

12) chain C
residue 161
type
ligand
sequence T
description binding site for residue GOL C 203
source : AC3

13) chain H
residue 10
type
ligand
sequence E
description binding site for residue GOL H 301
source : AC4

14) chain H
residue 19
type
ligand
sequence K
description binding site for residue GOL H 301
source : AC4

15) chain C
residue 82
type
ligand
sequence D
description binding site for residue GOL H 302
source : AC5

16) chain C
residue 84
type
ligand
sequence A
description binding site for residue GOL H 302
source : AC5

17) chain C
residue 85
type
ligand
sequence K
description binding site for residue GOL H 302
source : AC5

18) chain H
residue 33
type
ligand
sequence Y
description binding site for residue GOL H 302
source : AC5

19) chain H
residue 99
type
ligand
sequence S
description binding site for residue GOL H 302
source : AC5

20) chain H
residue 101
type
ligand
sequence G
description binding site for residue GOL H 302
source : AC5

21) chain C
residue 14-17
type binding
ligand GOL: GLYCEROL
sequence HCSS
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_201

22) chain C
residue 57
type binding
ligand GOL: GLYCEROL
sequence V
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_201

23) chain C
residue 65
type binding
ligand GOL: GLYCEROL
sequence N
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_201

24) chain C
residue 151
type binding
ligand GOL: GLYCEROL
sequence C
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_201

25) chain C
residue 16-18
type binding
ligand GOL: GLYCEROL
sequence SSN
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_202

26) chain C
residue 65
type binding
ligand GOL: GLYCEROL
sequence N
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_202

27) chain C
residue 94
type binding
ligand GOL: GLYCEROL
sequence S
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_202

28) chain C
residue 96
type binding
ligand GOL: GLYCEROL
sequence E
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_202

29) chain C
residue 40
type binding
ligand GOL: GLYCEROL
sequence P
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

30) chain C
residue 61
type binding
ligand GOL: GLYCEROL
sequence Q
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

31) chain C
residue 136-137
type binding
ligand GOL: GLYCEROL
sequence PS
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

32) chain C
residue 145-147
type binding
ligand GOL: GLYCEROL
sequence VNH
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

33) chain C
residue 158-161
type binding
ligand GOL: GLYCEROL
sequence CAST
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

34) chain C
residue 164
type binding
ligand GOL: GLYCEROL
sequence F
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_C_203

35) chain C
residue 46
type binding
ligand GOL: GLYCEROL
sequence R
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

36) chain C
residue 82
type binding
ligand GOL: GLYCEROL
sequence D
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

37) chain C
residue 84-85
type binding
ligand GOL: GLYCEROL
sequence AK
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

38) chain H
residue 33
type binding
ligand GOL: GLYCEROL
sequence Y
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

39) chain H
residue 99
type binding
ligand GOL: GLYCEROL
sequence S
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

40) chain H
residue 101-102
type binding
ligand GOL: GLYCEROL
sequence GR
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_302

41) chain H
residue 10
type binding
ligand GOL: GLYCEROL
sequence E
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_301

42) chain H
residue 12
type binding
ligand GOL: GLYCEROL
sequence K
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_301

43) chain H
residue 17-19
type binding
ligand GOL: GLYCEROL
sequence SVK
description GLYCEROL binding site
source pdb_hetatom : GOL_6d2p_H_301


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