SMTL ID : 4jb9.1

Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, G.121, I.156, L.161, H.220 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:T.120 Water bridges: A:T.120, A:T.120 NAG.2: 4 residues within 4Å: Chain A: E.40, N.113, K.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:N.113 NAG.3: 12 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, N.244, C.245, R.246, V.307, S.308 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 NAG.4: 5 residues within 4Å: Chain A: E.159, N.160 Chain C: N.30, S.31, F.90 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.31, C:S.31 NAG.5: 6 residues within 4Å: Chain A: E.153, I.154, N.173, K.174, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.174 Hydrogen bonds: A:E.153, A:I.154, A:N.173 NAG.6: 5 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198, A:K.303 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, T.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:N.202, A:T.204 NAG.8: 2 residues within 4Å: Chain A: N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain A: Q.256, N.259, C.262, G.270, C.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:G.270 NAG.10: 5 residues within 4Å: Chain A: K.136, N.146, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.146 Hydrogen bonds: A:S.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Georgiev, I.S. et al., Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Science (2013)

Release Date

2013-05-08

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
antibody VRC06 heavy chain: B
antibody VRC06 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

antibody VRC06 heavy chain

antibody VRC06 light chain

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