SMTL ID : 6o3d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: S.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.66, A:G.67 Water bridges: A:S.66, A:S.66 GOL.2: 4 residues within 4Å: Chain A: R.46, P.60, R.62, E.82 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.38, A:R.46, A:R.46, A:R.62, A:R.62, A:E.82, A:E.82 GOL.3: 5 residues within 4Å: Chain A: A.113, G.201, L.202, S.203 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.203 Water bridges: A:S.203, A:S.204, A:S.204 GOL.4: 5 residues within 4Å: Chain A: V.111, A.112, A.113, G.201 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.113 GOL.5: 10 residues within 4Å: Chain A: S.163, S.177, S.178, T.179 Chain B: F.177, P.178, V.180, S.188, L.189, S.190 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.163, A:S.177, A:S.177, A:T.179, B:F.177, B:S.190 Water bridges: A:T.179 GOL.6: 5 residues within 4Å: Chain A: S.122, D.123, E.124 Chain B: P.134, K.225 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.123, A:E.124, A:E.124, A:E.124 Water bridges: A:P.121 GOL.8: 6 residues within 4Å: Chain A: T.165, E.166, Q.167, D.168 Chain B: V.174, H.175 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.166, A:S.169, B:T.176, B:T.176 Hydrogen bonds: B:V.174, B:H.175 GOL.9: 2 residues within 4Å: Chain B: S.7, G.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.8 GOL.10: 7 residues within 4Å: Chain B: E.10, V.11, V.119, I.120, T.121, P.158, E.159 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.10, B:V.119, B:T.121, B:E.159 Water bridges: B:T.121, B:T.121 GOL.11: 5 residues within 4Å: Chain A: Y.50 Chain B: G.102, W.103, K.106, L.108 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.50, A:Y.50 Hydrogen bonds: B:W.103

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

SO4.7: 5 residues within 4Å: Chain B: G.27, T.28, F.29, S.30, T.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.29, B:S.30, B:S.30, B:T.31 Water bridges: B:S.30, 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 FAB LIGHT CHAIN: A
PGZL1 FAB HEAVY CHAIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

PGZL1 FAB LIGHT CHAIN

PGZL1 FAB HEAVY CHAIN

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