SMTL ID : 4lst.1

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade C strain ZM176.66 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: D.95, P.96, K.136, N.146, N.244, C.308, K.309, S.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:S.310 NAG.2: 6 residues within 4Å: Chain A: E.159, N.160 Chain C: Y.28, G.29, S.30, Y.89 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.28, C:S.30, C:Y.89, A:N.160 NAG.3: 5 residues within 4Å: Chain A: N.114, T.116, F.117, P.122, N.124 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.117 Hydrogen bonds: A:N.114, A:E.118, A:N.124 NAG.4: 2 residues within 4Å: Chain A: N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113 NAG.5: 2 residues within 4Å: Chain A: N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:N.253 NAG.6: 2 residues within 4Å: Chain A: T.261, N.263 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: N.259 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.259 NAG.8: 5 residues within 4Å: Chain A: E.203, N.207, N.259, Y.262 Ligands: NAG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.203, A:E.203, A:N.259, A:N.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies. Immunity (2013)

Release Date

2013-08-21

Peptides

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C: A
HEAVY CHAIN OF ANTIBODY VRC01: B
LIGHT CHAIN OF ANTIBODY VRC01: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C

HEAVY CHAIN OF ANTIBODY VRC01

LIGHT CHAIN OF ANTIBODY VRC01

Related Entries With Identical Sequence