SMTL ID : 3idx.1

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.6 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: S.49, N.51 Ligand excluded by PLIP NAG.3: 6 residues within 4Å: Chain A: N.84, T.86, F.87, N.88, T.94 Ligands: NAG.4 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.88, T.90, P.92 Ligands: NAG.3 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.83, N.95 Ligand excluded by PLIP NAG.6: 9 residues within 4Å: Chain A: E.65, P.66, N.116, N.202, I.268, R.269, S.271, S.272 Ligands: NAG.15 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.130, T.132, D.133 Ligand excluded by PLIP NAG.8: 7 residues within 4Å: Chain A: E.122, E.123, V.124, N.143, T.144, Q.169 Ligands: SO4.18 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.149, N.157, A.159 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: R.160, N.164, K.168, W.220 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.181, E.289 Ligands: NAG.14 Ligand excluded by PLIP NAG.12: 8 residues within 4Å: Chain A: V.197, N.211, T.213 Chain B: L.102, K.103, G.104 Ligands: NAG.13, SO4.20 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Q.214, N.217 Ligands: NAG.12 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.183, N.222 Ligands: NAG.11 Ligand excluded by PLIP NAG.15: 7 residues within 4Å: Chain A: E.147, R.269, S.271, S.272, N.273 Ligands: NAG.6, GOL.22 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.288 Ligand excluded by PLIP

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.17: 8 residues within 4Å: Chain A: E.195, Y.209, Q.247, I.248, I.249 Chain B: K.52, L.110, T.111 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.249, A:N.250, A:N.250, B:K.52, B:K.52 EPE.23: 7 residues within 4Å: Chain A: K.136, R.301 Chain B: R.30, R.72, D.73, N.74, S.75 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.136, A:R.301, B:R.30, B:N.74 Water bridges: A:D.299, B:R.30, B:N.74

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 2 residues within 4Å: Chain A: Q.169 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) SO4.19: 6 residues within 4Å: Chain A: I.105, P.107, V.108, N.303, W.304, E.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.108, A:V.108 Water bridges: A:S.306 SO4.20: 6 residues within 4Å: Chain A: Y.209, N.211, P.242, R.244 Chain B: I.109 Ligands: NAG.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.211 Water bridges: A:N.211, A:N.211, A:N.211 SO4.21: 3 residues within 4Å: Chain A: K.187, Q.188, R.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.188 Salt bridges: A:K.187, A:R.294

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 7 residues within 4Å: Chain A: N.116, G.117, L.119, S.145, N.273, T.275 Ligands: NAG.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.116, A:S.145, A:S.145 Water bridges: A:S.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, L. et al., Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science (2009)

Release Date

2009-11-17

Peptides

HIV-1 HxBc2 gp120 core: A
Fab b13 heavy chain: B
Fab b13 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 HxBc2 gp120 core

Fab b13 heavy chain

Fab b13 light chain

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