SMTL ID : 6o42.1 (1 other biounit)

Crystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in complex with MPER peptide epitope.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.161, S.163, S.177, S.178, T.179 Chain B: L.152, F.177, P.178, S.188, L.189, S.190 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.161, A:S.177, A:S.177, A:T.179, B:S.188, B:S.190 GOL.2: 5 residues within 4Å: Chain B: I.52, F.55, T.57, A.58 Chain C: W.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.52 GOL.3: 4 residues within 4Å: Chain B: Q.3, L.4, V.5, Q.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.4

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

SO4.4: 1 residues within 4Å: Chain B: K.217 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.217

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_gVmDmJ light chain: A
PGZL1_gVmDmJ heavy chain: B
MPER peptide, region 671-683 of HIV-1 gp41: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
G

PGZL1_gVmDmJ light chain

PGZL1_gVmDmJ heavy chain

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

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