SMTL ID : 2qsc.1

Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain B: N.28, S.31 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: N.138, N.139 Chain B: G.172, H.174, T.193 Ligands: CL.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.174 ZN.3: 2 residues within 4Å: Chain A: Q.24, H.70 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, H2O.1 ZN.5: 4 residues within 4Å: Chain B: D.54, E.56, T.57 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.54, B:E.56 ZN.6: 4 residues within 4Å: Chain B: T.88, E.89 Ligands: CL.7, CL.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.89

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: N.138, N.139 Chain B: H.174, T.193 Ligands: ZN.2 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: E.89 Ligands: ZN.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.87, T.88 Ligands: ZN.6 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: S.52, D.54, T.57 Ligands: ZN.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bell, C.H. et al., Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization. J.Mol.Biol. (2008)

Release Date

2008-01-15

Peptides

Fab F425-B4e8, Light chain: A
Fab F425-B4e8, Heavy chain: B
Envelope glycoprotein gp120: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
P

Fab F425-B4e8, Light chain

Fab F425-B4e8, Heavy chain

Envelope glycoprotein gp120