SMTL ID : 1rzk.1

HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.10, V.11, T.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.10 NAG.2: 2 residues within 4Å: Chain A: L.47, N.55 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: N.92, T.94, P.96, Q.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.92, A:T.94, A:T.94, A:Q.181 NAG.4: 2 residues within 4Å: Chain A: L.8, N.99 No protein-ligand interaction detected (PLIP) NAG.5: 6 residues within 4Å: Chain A: N.120, N.206, C.266, S.267, S.268 Ligands: NAG.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.206, A:S.267 Water bridges: A:E.69, A:E.69, A:E.69, A:N.206 NAG.6: 3 residues within 4Å: Chain A: N.134, T.136, N.137 No protein-ligand interaction detected (PLIP) NAG.7: 6 residues within 4Å: Chain A: E.126, E.127, I.128, N.147, Q.173, K.177 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.173 Hydrogen bonds: A:E.127, A:I.128, A:N.147, A:Q.173 NAG.8: 5 residues within 4Å: Chain A: N.153, N.161, N.234, R.265, S.267 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.161 Hydrogen bonds: A:N.234, A:R.265, A:R.265, A:S.267 NAG.9: 1 residues within 4Å: Chain A: N.185 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.185 NAG.10: 4 residues within 4Å: Chain A: N.215, T.217, Q.218, P.238 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.238 Hydrogen bonds: A:T.217 NAG.11: 4 residues within 4Å: Chain A: T.221, N.223, K.227, L.228 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.228 Hydrogen bonds: A:T.221, A:N.223 NAG.12: 4 residues within 4Å: Chain A: K.164, N.229, G.232, R.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.229, A:R.233 NAG.13: 4 residues within 4Å: Chain A: V.151, S.267, N.269 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.267 NAG.14: 1 residues within 4Å: Chain A: N.284 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.C. et al., Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-02-03

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
G

B
C

C
L

D
H

ENVELOPE GLYCOPROTEIN GP120

T-CELL SURFACE GLYCOPROTEIN CD4

ANTIBODY 17B, LIGHT CHAIN

ANTIBODY 17B, HEAVY CHAIN

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