SMTL ID : 6cdo.1

Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1 fusion peptide residue 512-519

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

ALA-VAL-GLY-ILE-GLY-ALA-VAL-PHE.1: 17 residues within 4Å: Chain A: E.33, A.50, D.52, S.55, A.57, S.58, A.59, L.99, Y.101, F.102, G.103, Y.104 Chain B: Y.31, Y.37, E.39, G.96, Y.101 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.31, B:Y.31, B:Y.37, B:Y.101, A:A.57, A:L.99, A:Y.101, A:F.102, A:F.102 Hydrogen bonds: B:E.39, B:G.96, B:Y.101, A:E.33, A:E.33, A:F.102 Water bridges: A:Y.101

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

SO4.2: 4 residues within 4Å: Chain A: T.40, P.41, V.42, R.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.40, A:T.40, A:V.42, A:R.43 Salt bridges: A:R.43 SO4.3: 4 residues within 4Å: Chain A: Q.6, S.7, G.8, K.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.8 Water bridges: A:A.9, A:A.9 Salt bridges: A:K.206 SO4.4: 4 residues within 4Å: Chain A: S.133, K.134, K.223 Chain B: K.212 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.133 Water bridges: A:K.134 Salt bridges: A:K.134, A:K.223, B:K.212 SO4.5: 3 residues within 4Å: Chain A: P.14, S.117, S.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.118 SO4.6: 3 residues within 4Å: Chain A: S.25, G.26, Y.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.26, A:Y.27 SO4.7: 2 residues within 4Å: Chain A: R.13, S.120 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.13, A:R.13 Salt bridges: A:R.13 SO4.8: 3 residues within 4Å: Chain B: P.8, L.9, S.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.9, B:S.10, B:S.10 SO4.9: 1 residues within 4Å: Chain B: S.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.57, B:S.57 SO4.10: 3 residues within 4Å: Chain B: S.57, R.58, R.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.59 Salt bridges: B:R.59 SO4.11: 3 residues within 4Å: Chain B: Y.31, S.97, H.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.99 Salt bridges: B:H.98

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

2018-05-16

Peptides

vFP16.02 Fab heavy chain: A
vFP16.02 Fab light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

vFP16.02 Fab heavy chain

vFP16.02 Fab light chain