SMTL ID : 6o41.3 (2 other biounits)

Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: Q.161, E.162, S.163, S.177, T.179 Chain B: F.177, P.178, S.188, L.189, S.190 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.178, B:S.188, B:S.190, A:S.177, A:T.179, A:T.179 GOL.2: 6 residues within 4Å: Chain A: V.86, Y.88, Q.101 Chain B: G.42, Q.43, G.44 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.88 Water bridges: A:R.104, B:G.44, B:G.44 GOL.3: 7 residues within 4Å: Chain B: K.128, G.129, T.216 Chain C: T.21, T.22, T.23, Y.38 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.128, B:K.128, B:G.129, B:T.216, B:T.216, C:T.23 Water bridges: C:Y.38, C:Y.38

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

germline PGZL1_gVmDmJ light chain: A
germline PGZL1_gVmDmJ heavy chain: B
Immunoglobulin G-binding protein G (DOMAIN III): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
N

germline PGZL1_gVmDmJ light chain

germline PGZL1_gVmDmJ heavy chain

Immunoglobulin G-binding protein G (DOMAIN III)

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