SMTL ID : 2ny3.1

HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4 and Antibody 17b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain C: T.99, F.100, Q.102 Chain D: Q.43, G.44, L.45, E.46, H.63 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Water bridges: D:R.38, D:E.46, D:W.47, D:W.47, D:R.38, D:E.46, D:E.46, D:E.46 Hydrogen bonds: C:F.100, C:F.100, C:Q.102, D:Q.43, D:G.44, D:L.45, C:Q.102

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

NAG.2: 2 residues within 4Å: Chain A: V.5, N.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.5 NAG.3: 1 residues within 4Å: Chain A: N.51 No protein-ligand interaction detected (PLIP) NAG.4: 6 residues within 4Å: Chain A: N.84, T.86, P.92, T.94, E.122 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.86, A:P.92, A:T.94 Water bridges: A:N.84 NAG.5: 4 residues within 4Å: Chain A: F.87, N.88, T.90 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.88, A:T.90 Water bridges: A:N.84 NAG.6: 2 residues within 4Å: Chain A: N.83, N.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95, A:N.95 NAG.7: 11 residues within 4Å: Chain A: E.65, P.66, R.106, V.108, L.115, N.116, N.202, C.270, S.271, S.272 Ligands: NAG.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.108, A:L.115 Hydrogen bonds: A:R.106, A:N.116, A:S.272 Water bridges: A:N.202 NAG.8: 3 residues within 4Å: Chain A: N.130, T.132, D.133 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.130 Water bridges: B:K.30, B:K.30 NAG.9: 7 residues within 4Å: Chain A: E.122, E.123, V.124, N.143, T.144, Q.169, K.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.123, A:V.124, A:N.143 NAG.10: 5 residues within 4Å: Chain A: E.147, N.149, N.157, I.158, A.159 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.157 Water bridges: A:A.159, A:K.162 NAG.11: 3 residues within 4Å: Chain A: N.164, K.168, W.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.168 NAG.12: 3 residues within 4Å: Chain A: V.197, N.211, T.213 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.197 Hydrogen bonds: A:N.211 Water bridges: A:Q.188, A:Q.188, A:Q.188, A:Q.188, A:T.213 NAG.13: 2 residues within 4Å: Chain A: T.213, N.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.213 Hydrogen bonds: A:N.217 NAG.14: 4 residues within 4Å: Chain A: S.145, S.271, N.273 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.145, A:N.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature (2007)

Release Date

2007-02-06

Peptides

ENVELOPE GLYCOPROTEIN GP120: A
T-cell surface glycoprotein CD4: B
ANTIBODY 17B, LIGHT CHAIN: C
ANTIBODY 17B, HEAVY CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ENVELOPE GLYCOPROTEIN GP120

T-cell surface glycoprotein CD4

ANTIBODY 17B, LIGHT CHAIN

ANTIBODY 17B, HEAVY CHAIN

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