SMTL ID : 7rdw.2 (3 other biounits)

Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 9 residues within 4Å: Chain A: F.94, E.95, L.145, N.146, N.245, G.247, C.313, S.314, S.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.247

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: N.81, N.293, V.298, K.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.293 NAG.3: 3 residues within 4Å: Chain A: N.160, T.162, D.163 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.163 Hydrogen bonds: A:T.162 NAG.4: 4 residues within 4Å: Chain A: N.179, T.181, R.312, S.314 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.181, A:R.312 NAG.5: 3 residues within 4Å: Chain A: N.254, T.256, P.285 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.254, A:T.256, A:T.256 NAG.6: 3 residues within 4Å: Chain A: R.136, G.147, N.316 No protein-ligand interaction detected (PLIP)

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.7: 1 residues within 4Å: Chain A: T.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.80

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 1 residues within 4Å: Chain A: I.227 No protein-ligand interaction detected (PLIP)

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

SO4.9: 4 residues within 4Å: Chain A: I.288, K.289, Q.290, I.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.290, A:I.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gray, M.D. et al., Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain. Sci Adv (2022)

Release Date

2022-05-25

Peptides

Glycoprotein 120: A
FH1 Fab Heavy Chain: B
FH1 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
U

C
V

Glycoprotein 120

FH1 Fab Heavy Chain

FH1 Fab Light Chain

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