SMTL ID : 7ri2.1

Crystal structure of anti-HIV llama VHH antibody A12 in complex with HIV-1 C1086 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.142, T.144, P.146, I.180, S.182, H.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.142 NAG.2: 1 residues within 4Å: Chain A: N.149 No protein-ligand interaction detected (PLIP) NAG.3: 6 residues within 4Å: Chain A: D.119, V.162, N.170, C.333, N.334, S.335 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.162 Hydrogen bonds: A:N.170 NAG.4: 3 residues within 4Å: Chain A: N.184, T.186, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.186 NAG.5: 5 residues within 4Å: Chain A: E.176, E.177, I.178, N.197, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.178, A:E.198, A:E.240 NAG.6: 3 residues within 4Å: Chain A: T.264, N.277, S.279 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.264 Hydrogen bonds: A:N.277 NAG.7: 6 residues within 4Å: Chain A: P.254, D.280, N.283, H.293, T.294, G.295 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.254 Hydrogen bonds: A:G.295 NAG.8: 3 residues within 4Å: Chain A: S.247, R.287, N.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.288

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

Glycoprotein 120: A
anti-HIV llama VHH antibody A12: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycoprotein 120

anti-HIV llama VHH antibody A12

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