SMTL ID : 6o3k.1

Crystal structure of the unbound Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: P.8, G.9, T.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.9, A:T.10 Water bridges: A:Q.6 GOL.2: 4 residues within 4Å: Chain A: Y.50, S.53, G.54, R.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.50, A:S.53, A:R.55 Water bridges: A:Y.50 GOL.3: 5 residues within 4Å: Chain A: S.122, D.123, E.124 Chain B: P.134, A.136 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.223 Hydrogen bonds: A:D.123, A:D.123, A:E.124 GOL.4: 6 residues within 4Å: Chain A: V.151, Q.156, N.159, L.182, D.186, H.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.159, A:D.186 GOL.6: 11 residues within 4Å: Chain A: Q.161, S.163, S.177, S.178, T.179 Chain B: F.177, P.178, V.180, S.188, L.189, S.190 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.177, B:S.188, B:S.190, A:S.163, A:S.177, A:T.179 GOL.7: 6 residues within 4Å: Chain A: Y.50, A.56, T.57 Chain B: E.101, L.108, E.112 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Water bridges: B:E.101, B:E.101, B:E.112, A:T.57, A:T.57, A:T.57, A:T.57 Hydrogen bonds: A:T.57 GOL.8: 7 residues within 4Å: Chain B: E.159, P.160, V.161, F.177, P.178, A.179, L.189 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.156, B:E.159, B:V.161, B:V.161, B:F.177, B:A.179 GOL.9: 4 residues within 4Å: Chain B: V.93, Q.116, G.117, L.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.116 Water bridges: B:Q.116, B:L.119

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

SO4.5: 3 residues within 4Å: Chain A: P.60, G.61, R.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.61, A:R.62 Salt bridges: A:R.62 SO4.10: 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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

PGZL1.H4K3 light chain

PGZL1.H4K3 heavy chain

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