SMTL ID : 7rdw.3 (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: 7 residues within 4Å: Chain C: F.94, L.145, N.146, G.247, R.312, S.314, S.315 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.94, C:G.247

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

NH4.2: 1 residues within 4Å: Chain A: F.106 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain C: N.81, V.298 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.298 Hydrogen bonds: C:N.81 NAG.4: 5 residues within 4Å: Chain C: N.114, T.116, F.117, N.118 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.117 Hydrogen bonds: C:N.118 NAG.5: 3 residues within 4Å: Chain C: N.118, T.120 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.120 NAG.6: 5 residues within 4Å: Chain C: V.42, N.113, N.114, N.125, S.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.125, C:S.127 NAG.7: 3 residues within 4Å: Chain C: N.160, T.162, D.163 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.163 NAG.8: 5 residues within 4Å: Chain C: E.153, V.154, N.173, T.174, K.216 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.174 Hydrogen bonds: C:V.154, C:V.154 NAG.9: 3 residues within 4Å: Chain C: E.177, I.178, N.179 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.178 NAG.10: 2 residues within 4Å: Chain C: N.207 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.207 NAG.11: 3 residues within 4Å: Chain C: T.241, N.254, T.256 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.241 Hydrogen bonds: C:N.254 NAG.12: 3 residues within 4Å: Chain C: R.136, G.147, N.316 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.316

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

EDO.13: 5 residues within 4Å: Chain C: N.207, K.211, I.227, I.228 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.207, C:I.227

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
I

C
N

FH1 Fab Heavy Chain

FH1 Fab Light Chain

Glycoprotein 120

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