SMTL ID : 6o3u.2 (3 other biounits)

Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with 06:0 PA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: P.8, G.9, T.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.9, A:T.10 GOL.2: 3 residues within 4Å: Chain A: Q.38, K.40, Q.43 No protein-ligand interaction detected (PLIP) GOL.3: 4 residues within 4Å: Chain A: P.60, G.61, R.62, R.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.61, A:R.62, A:R.62, A:R.78

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

SO4.4: 10 residues within 4Å: Chain A: Q.161, E.162, S.163, S.177, T.179 Chain B: F.177, V.180, S.188, L.189, S.190 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.161, A:S.163, A:S.177, A:T.179, B:S.190, B:S.190, B:S.190 SO4.5: 2 residues within 4Å: Chain B: K.13, S.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.126 Salt bridges: B:K.13 SO4.6: 5 residues within 4Å: Chain A: Y.50, Y.92 Chain B: R.106, L.108, R.109 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.106, B:R.109 SO4.7: 2 residues within 4Å: Chain B: Q.43, R.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44 Salt bridges: B:R.44 SO4.8: 2 residues within 4Å: Chain B: R.63, R.67 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.63, B:R.67

2 x 44E: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate(Non-covalent)

44E.9: 4 residues within 4Å: Chain B: A.72, D.73, R.74, S.75 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.72, B:D.73, B:D.73, B:R.74, B:S.75 Salt bridges: B:R.74 44E.10: 4 residues within 4Å: Chain B: S.28, F.29, S.30, L.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: 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
A

B
B

PGZL1.H4K3 light chain

PGZL1.H4K3 heavy chain

Related Entries With Identical Sequence