SMTL ID : 6o3l.2 (1 other biounit)

Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with its MPER peptide epitope (region 671-683 of HIV-1 gp41).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: T.165, E.166, D.168 Chain B: V.174, H.175 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:T.176, A:T.165, A:E.166, A:E.166, A:Q.167, A:S.169 Salt bridges: B:H.175 Hydrogen bonds: A:E.166, A:D.168 PO4.2: 3 residues within 4Å: Chain B: S.28, F.29, S.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.28, B:F.29, B:S.30 PO4.3: 6 residues within 4Å: Chain A: Y.50, G.51, Y.92 Chain B: R.106, L.108, R.109 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.108, A:Y.92 Salt bridges: B:R.106, B:R.109

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: N.210, K.212, N.215, K.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.210, B:N.210 GOL.5: 3 residues within 4Å: Chain A: S.95 Chain C: N.1, W.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.95, C:N.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun (2019)

Release Date

2019-12-04

Peptides

PGZL1.H4K3 light chain: A
PGZL1.H4K3 heavy chain: B
MPER peptide, region 671-683 of HIV-1 gp41: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
E

PGZL1.H4K3 light chain

PGZL1.H4K3 heavy chain

MPER peptide, region 671-683 of HIV-1 gp41

Related Entries With Identical Sequence