SMTL ID : 2ny4.1

HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, 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: 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 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.63, C:D.1, C:F.100, C:F.100, C:Q.102, D:Q.43, D:G.44, D:L.45, C:Q.102 Water bridges: D:W.47, C:D.1, D:E.46

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

NAG.2: 1 residues within 4Å: Chain A: N.6 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.51 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: N.84, T.86, P.92 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.84 Water bridges: A:T.86, A:P.92 NAG.5: 4 residues within 4Å: Chain A: N.88, T.90, S.128 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.90 Water bridges: A:N.88, A:N.88 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:E.121 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.115 Hydrogen bonds: A:E.65, A:R.106, A:R.106, A:N.116, A:S.272 Water bridges: A:S.271 NAG.8: 3 residues within 4Å: Chain A: N.130, T.132, D.133 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.130 Water bridges: A:T.132, A:N.134, A:N.134, B:K.30 NAG.9: 7 residues within 4Å: Chain A: C.122, E.123, V.124, N.143, T.144, Q.169, K.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:N.143, A:T.144, A:T.144 NAG.10: 5 residues within 4Å: Chain A: E.147, N.149, N.157, I.158, A.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.147, A:E.147, A:N.149 Water bridges: A:N.157 NAG.11: 4 residues within 4Å: Chain A: R.160, N.164, K.168, W.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.168, A:K.168 NAG.12: 3 residues within 4Å: Chain A: V.197, N.211, T.213 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.188, A:N.211, 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

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.15: 6 residues within 4Å: Chain A: T.198, Y.209, N.211, P.242, C.243, R.244 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.242

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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