SMTL ID : 5ukr.1

Structure of unliganded anti-gp120 CD4bs antibody DH522.2 Fab in complex with a gp120 core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain C: V.112, L.119, N.120, N.206, C.207, S.267, S.268 Ligands: NAG.6 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.112, C:L.119 Hydrogen bonds: C:S.268 NAG.2: 2 residues within 4Å: Chain C: N.134, N.137 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain C: V.151, N.153, N.234, S.267 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.267 NAG.4: 2 residues within 4Å: Chain C: H.159, N.161 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: F.56 Chain C: V.201, N.215 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: S.267, N.269 Ligands: NAG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, W.B. et al., Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations. Nat Commun (2017)

Release Date

2017-12-06

Peptides

DH522.2 Fab fragment heavy chain: A
DH522.2 Fab fragment light chain: B
Chimeric B.YU2 gp120 core derived from HIV-1 Env: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

DH522.2 Fab fragment heavy chain

DH522.2 Fab fragment light chain

Chimeric B.YU2 gp120 core derived from HIV-1 Env

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