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

Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.39 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain C: S.12, N.102, T.104 No protein-ligand interaction detected (PLIP)

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

NAG.2: 7 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, S.158, H.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:T.120, A:T.120 NAG.3: 4 residues within 4Å: Chain A: H.42, E.44, N.113, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44, A:N.113 NAG.4: 9 residues within 4Å: Chain A: P.96, V.138, L.145, N.146, N.244, C.245, R.246, V.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:D.95, A:R.246, A:S.308 NAG.5: 3 residues within 4Å: Chain A: N.160 Chain C: G.29, F.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 NAG.6: 3 residues within 4Å: Chain A: M.240, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: Q.229, P.230, T.255, N.259 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, X. et al., Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell (2015)

Release Date

2015-04-29

Peptides

Envelope glycoprotein gp160,Envelope glycoprotein gp160: A
HEAVY CHAIN OF ANTIBODY VRC06B: B
LIGHT CHAIN OF ANTIBODY VRC06B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

Envelope glycoprotein gp160,Envelope glycoprotein gp160

HEAVY CHAIN OF ANTIBODY VRC06B

LIGHT CHAIN OF ANTIBODY VRC06B

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