SMTL ID : 2ny7.1 (4 other biounits)

HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.88, T.90, G.91, P.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 NAG.2: 3 residues within 4Å: Chain A: V.3, N.83, N.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83, A:N.95 NAG.3: 10 residues within 4Å: Chain A: R.106, P.107, L.115, N.116, F.201, N.202, C.203, S.271, S.272 Ligands: NAG.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.107, A:L.115, A:F.201 Hydrogen bonds: A:S.272 Water bridges: A:N.116 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: 7 residues within 4Å: Chain A: E.122, E.123, V.124, N.143, T.144, Q.169, K.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.124, A:Q.169 NAG.6: 4 residues within 4Å: Chain A: E.147, N.149, I.158, A.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 NAG.7: 3 residues within 4Å: Chain A: R.160, N.164, W.225 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.180, N.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.181 NAG.9: 8 residues within 4Å: Chain A: Q.188, N.211, T.213, Q.214, P.242 Chain B: S.103, W.104 Ligands: NAG.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.242 Hydrogen bonds: A:T.213, B:W.104 Water bridges: A:Q.188, A:Q.188, A:Q.214 NAG.10: 3 residues within 4Å: Chain A: T.213, N.217 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.217 NAG.11: 5 residues within 4Å: Chain A: T.183, I.185, T.219, N.222, S.223 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.185, A:T.219 Hydrogen bonds: A:T.219, A:T.219, A:S.223 NAG.12: 4 residues within 4Å: Chain A: N.116, S.145, N.273 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.145 Water bridges: A:N.273 NAG.13: 1 residues within 4Å: Chain A: N.288 No protein-ligand interaction detected (PLIP)

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
ANTIBODY b12, HEAVY CHAIN: B
ANTIBODY b12, LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120

ANTIBODY b12, HEAVY CHAIN

ANTIBODY b12, LIGHT CHAIN

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