SMTL ID : 1gc1.1

HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: N.92, T.94, P.96 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.92 Water bridges: A:N.92, A:N.92, A:N.92 NAG-FUC.2: 7 residues within 4Å: Chain A: E.151, N.153, N.161, I.162, S.163, R.273 Ligands: NAG-FUC.4 9 PLIP interactions: 9 interactions with chain A Water bridges: A:E.151, A:E.151, A:N.153, A:N.153, A:N.161, A:N.161, A:S.163, A:S.163, A:K.166 NAG-FUC.3: 7 residues within 4Å: Chain A: R.164, T.217, Q.218, N.221, T.242, I.243 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.164, A:R.164, A:Q.218, A:Q.218, A:T.242, A:Q.218 Water bridges: A:N.221 NAG-FUC.4: 5 residues within 4Å: Chain A: E.151, N.153, S.275, N.277 Ligands: NAG-FUC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.151 Hydrogen bonds: A:E.151, A:N.277 Water bridges: A:N.277, A:N.277

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

NAG.5: 2 residues within 4Å: Chain A: P.46, N.55 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.46 NAG.6: 4 residues within 4Å: Chain A: R.110, N.120, S.275, S.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:N.120, A:S.276 NAG.7: 4 residues within 4Å: Chain A: N.134, T.136, D.137, K.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.134, A:D.137, A:D.137, A:K.140, A:K.140 NAG.8: 5 residues within 4Å: Chain A: E.126, E.127, V.128, N.147, Q.173 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.127 Hydrogen bonds: A:V.128, A:N.147 NAG.9: 7 residues within 4Å: Chain A: N.153, C.154, T.155, H.159, C.160, N.161, T.244 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.159, A:N.161, A:T.244 Hydrogen bonds: A:N.153, A:T.155, A:H.159, A:H.159 NAG.10: 11 residues within 4Å: Chain A: R.164, N.168, L.171, Q.218, L.219, N.221, S.222, W.224, I.243 Ligands: NAG-FUC.3, NAG-FUC.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.164, A:N.168, A:S.222, A:S.222 Water bridges: A:Q.218, A:N.221 NAG.11: 3 residues within 4Å: Chain A: N.215, T.217, Q.218 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.218 Hydrogen bonds: A:T.217, A:Q.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwong, P.D. et al., Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature (1998)

Release Date

1998-07-08

Peptides

ENVELOPE PROTEIN GP120: A
CD4: B
ANTIBODY 17B: C
ANTIBODY 17B: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
C

C
L

D
H

ENVELOPE PROTEIN GP120

CD4

ANTIBODY 17B

ANTIBODY 17B

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