SMTL ID : 6pds.2 (1 other biounit)

Vaccine-elicited NHP FP-targeting antibody 0PV-a.04 in complex with HIV fusion peptide (residue 512-519)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-mer

Ligands

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

ALA-VAL-GLY-ILE-GLY-ALA-VAL.1: 15 residues within 4Å: Chain A: F.35, Y.54, E.101, R.102, V.103, V.104 Chain B: N.32, S.34, R.46, H.49, Y.91, E.92, N.93, F.94, I.96 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:H.49, B:Y.91, B:Y.91, B:F.94, B:F.94, B:F.94, B:I.96, A:Y.54, A:E.101 Hydrogen bonds: B:Y.91, A:Y.54, A:Y.54, A:V.104 Water bridges: B:N.32, B:E.92, A:A.105

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

SO4.2: 3 residues within 4Å: Chain A: D.215, K.216, R.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.217 Water bridges: A:R.217, A:R.217 Salt bridges: A:K.216, A:R.217 SO4.3: 2 residues within 4Å: Chain B: P.59, S.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.60 Water bridges: B:S.60, B:S.60, B:R.61, B:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies. To Be Published

Release Date

2020-06-24

Peptides

antibody 0PV-a.04 heavy chain: A
antibody 0PV-a.04 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

antibody 0PV-a.04 heavy chain

antibody 0PV-a.04 light chain

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