SMTL ID : 6o41.1 (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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: Q.161, E.162, S.163, S.177, S.178, T.179 Chain B: F.177, P.178, S.188, L.189, S.190 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.161, A:S.163, A:T.179, B:F.177, B:S.188, B:S.190 GOL.2: 7 residues within 4Å: Chain A: T.165, E.166, D.168, T.173 Chain B: V.174, H.175, T.176 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.176, A:D.168, A:D.168, A:T.173 Water bridges: B:V.174, B:T.176 GOL.3: 4 residues within 4Å: Chain A: Y.33, G.93, T.94, S.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.94, A:S.95, A:S.95 GOL.4: 4 residues within 4Å: Chain A: R.109, K.170, D.171, S.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.172, A:S.172 Water bridges: A:K.108 GOL.5: 6 residues within 4Å: Chain A: Q.38, Q.39, K.40, Q.43, A.44, R.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.40, A:R.46, A:R.46 Water bridges: A:A.44 GOL.6: 7 residues within 4Å: Chain B: R.38, Q.39, A.40, Q.43, G.44, E.46, K.63 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:A.40, B:A.40, B:G.44, B:K.63 GOL.7: 8 residues within 4Å: Chain B: Y.156, E.159, P.160, V.161, F.177, P.178, A.179, L.189 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.156, B:V.161, B:V.161, B:F.177, B:A.179

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
L

B
H

C
M

germline PGZL1_gVmDmJ light chain

germline PGZL1_gVmDmJ heavy chain

Immunoglobulin G-binding protein G (DOMAIN III)

Related Entries With Identical Sequence