SMTL ID : 2ny5.1

HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) Complexed with CD4 and Antibody 17b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 9 residues within 4Å: Chain C: D.1, T.99, F.100, Q.102 Chain D: Q.43, G.44, L.45, E.46, H.63 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:F.100, C:F.100, D:H.63, D:Q.43, D:G.44, D:L.45, D:E.46, C:Q.102, C:Q.102 Water bridges: D:W.47, D:W.47, D:H.63

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

NAG.2: 2 residues within 4Å: Chain A: N.88, T.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.88, A:P.92 NAG.3: 9 residues within 4Å: Chain A: E.65, V.108, L.115, N.116, N.202, C.270, S.271, S.272 Ligands: NAG.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.108, A:L.115 Hydrogen bonds: A:E.65, A:E.65, A:N.116, A:S.272 Water bridges: A:R.106, A:G.204 NAG.4: 3 residues within 4Å: Chain A: N.130, T.132, D.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.130 NAG.5: 6 residues within 4Å: Chain A: E.122, E.123, V.124, N.143, T.144, K.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.124, A:N.143 NAG.6: 5 residues within 4Å: Chain A: N.149, N.157, I.158, A.159, S.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.271 Water bridges: A:E.147, A:A.159 NAG.7: 2 residues within 4Å: Chain A: N.164, K.168 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: V.197, N.211, T.213 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.197 Water bridges: A:N.211, A:N.211 NAG.9: 1 residues within 4Å: Chain A: N.217 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.217, A:N.217, A:N.217, A:N.217 NAG.10: 3 residues within 4Å: Chain A: S.271, N.273 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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
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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