SMTL ID : 7r74.2 (1 other biounit)

Crystal structure of llama VHH antibody in complex with HIV-1 HXBC2 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain B: E.177, N.179, S.202, R.312, S.314 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.177, B:N.179, B:R.312, B:R.312, B:S.314 NAG.2: 2 residues within 4Å: Chain B: N.207, K.211 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain B: N.118, T.120, P.122, S.158 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain B: V.42, N.113, K.115, N.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.125 NAG.5: 4 residues within 4Å: Chain B: N.146, S.175, N.316 Ligands: NAG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.175, B:N.316 NAG.6: 9 residues within 4Å: Chain B: P.96, R.136, V.138, L.145, N.146, N.245, S.314, S.315 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.138, B:L.145 Hydrogen bonds: B:S.315 NAG.7: 2 residues within 4Å: Chain B: N.254, T.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.254, B:T.256 NAG.8: 2 residues within 4Å: Chain B: N.160, T.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.160 NAG.9: 3 residues within 4Å: Chain B: E.152, N.173, Q.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.173, B:T.174, B:Q.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure (2022)

Release Date

2022-03-30

Peptides

Antibody C8 VHH domain: A
Glycoprotein 120: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Antibody C8 VHH domain

Glycoprotein 120

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