SMTL ID : 3idy.2 (1 other biounit)

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

28 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: 5 residues within 4Å: Chain A: N.84, T.86, N.88, T.94 Ligands: NAG.3 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain A: F.87, N.88, T.90, P.92 Ligands: NAG.2 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.83, N.95 Ligand excluded by PLIP NAG.5: 8 residues within 4Å: Chain A: E.65, V.108, N.116, N.202, R.269, S.271, S.272 Ligands: NAG.13 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.130, T.132, D.133 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: E.122, E.123, V.124, N.143, Q.169 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: E.147, N.149, A.159 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: R.160, N.164, W.220 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.181, F.221, S.223, E.289 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: V.197, N.211, T.213 Chain B: L.102, G.104 Ligands: NAG.12 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: T.213, N.217 Ligands: NAG.11 Ligand excluded by PLIP NAG.13: 7 residues within 4Å: Chain A: S.145, E.147, R.269, S.271, S.272, N.273 Ligands: NAG.5 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.285, S.286, N.288, E.289, S.290 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain D: N.6 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain D: N.84, T.86, N.88, T.94 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: N.88, T.90, F.131 Ligands: NAG.17 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: N.83, N.95 Ligand excluded by PLIP NAG.20: 9 residues within 4Å: Chain D: E.65, V.108, N.116, N.202, I.268, R.269, S.271, S.272 Ligands: NAG.28 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.130 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: E.122, E.123, V.124, N.143 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain D: E.147, N.149, I.158, A.159 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.164, W.220 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain D: N.181, T.183, F.221, N.222, S.223, E.289 Ligand excluded by PLIP NAG.26: 7 residues within 4Å: Chain D: V.197, N.211, T.213 Chain E: L.102, G.104, Y.107 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.217 Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain D: E.147, R.269, S.271, S.272, N.273 Ligands: NAG.20 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.287, N.288 Ligand excluded by PLIP

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

SO4.15: 2 residues within 4Å: Chain A: K.187, R.294 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.188 Water bridges: A:K.187, A:K.187, A:R.294, A:R.294 Salt bridges: A:K.187, A:R.294

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: AD
Fab b13 heavy chain: BE
Fab b13 light chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

D
A

B
H

E
B

C
L

F
C

HIV-1 HxBc2 gp120 core

Fab b13 heavy chain

Fab b13 light chain

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