eF-site ID 6d2p-H
PDB Code 6d2p
Chain H

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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 H:  QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQA
PGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAY
MELSRLRSDDTAVYYCARSLGRDWFDPWGQGTLVTVSSAS
TKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP
SNTKVDKKVEPKS
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 H
residue 10
type
ligand
sequence E
description binding site for residue GOL H 301
source : AC4

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

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

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

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

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

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

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

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

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

11) 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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