SMTL ID : 5vgj.1

Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90, bound to a scaffolded WITO V1V2 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.46 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 20 residues within 4Å: Chain A: V.17, T.18, N.37, Y.59, L.61 Chain B: D.31, S.53, S.54, D.56, Y.58, S.101, G.102, W.103, F.104, Y.105, H.106 Chain C: Q.98, T.99, P.100, R.101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.99, C:Q.98 NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 18 residues within 4Å: Chain A: T.11, H.13, S.39, F.40, N.41, K.57, G.128 Chain B: E.1, E.27, N.32, R.97, G.98, P.99, E.100, Y.107, W.109, G.110 Chain C: Y.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.54, C:Y.54

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain A: I.46, G.47, N.48, S.49, D.53, F.133 No protein-ligand interaction detected (PLIP)

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

NAG.4: 6 residues within 4Å: Chain A: N.16, E.33, K.64 Chain C: G.32, N.33, G.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:E.33, A:K.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cale, E.M. et al., Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop. Immunity (2017)

Release Date

2017-05-31

Peptides

1FD6-V1V2-WITO: A
VRC38.01 Fab Heavy Chain: B
VRC38.01 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

1FD6-V1V2-WITO

VRC38.01 Fab Heavy Chain

VRC38.01 Fab Light Chain

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