SMTL ID : 5tkj.2 (3 other biounits)

Structure of vaccine-elicited diverse HIV-1 neutralizing antibody vFP1.01 in complex with HIV-1 fusion peptide residue 512-519

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- VAL- GLY- ILE- GLY- ALA- VAL- PHE: HIV-1 fusion peptide residue 512-519(Non-covalent)

ALA-VAL-GLY-ILE-GLY-ALA-VAL-PHE.1: 18 residues within 4Å: Chain A: E.33, A.50, V.52, Y.57, T.58, A.59, L.99, N.101, Y.102, W.103, Y.104 Chain B: Y.31, S.32, Y.37, E.39, F.94, G.96, Y.101 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:A.50, A:V.52, A:Y.57, A:L.99, A:Y.102, B:Y.31, B:Y.37, B:F.94, B:Y.101 Hydrogen bonds: A:E.33, A:E.33, A:E.33, A:Y.102, B:E.39, B:G.96, B:Y.101 Water bridges: A:E.33, A:E.33, A:Y.102, B:Y.101

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.84, R.85 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.84, A:R.85 Salt bridges: A:R.84, A:R.85 SO4.3: 1 residues within 4Å: Chain A: R.85 6 PLIP interactions: 6 interactions with chain A Water bridges: A:S.17, A:R.84, A:R.84, A:R.85, A:R.85 Salt bridges: A:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Nat. Med. (2018)

Release Date

2018-04-04

Peptides

vFP1.01 chimeric mouse antibody heavy chain: A
vFP1.01 chimeric mouse antibody light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

vFP1.01 chimeric mouse antibody heavy chain

vFP1.01 chimeric mouse antibody light chain

Related Entries With Identical Sequence