SMTL ID : 6mg7.1

Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1 CLADE A/E GP120 and M48U1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: E.57, N.58 Chain C: M.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.57, A:N.58 NAG.2: 8 residues within 4Å: Chain A: N.131, T.133, G.134, P.135, I.169, S.171, L.174, H.233 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.174 Hydrogen bonds: A:N.131 NAG.3: 3 residues within 4Å: Chain A: H.55, N.126, N.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.55 NAG.4: 7 residues within 4Å: Chain A: P.109, K.149, L.158, N.159, C.319, V.320, S.321 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.158 Hydrogen bonds: A:K.149, A:S.321 NAG.5: 6 residues within 4Å: Chain A: E.165, E.166, I.167, N.186, Q.225, K.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.167, A:N.186, A:Q.225, A:Q.225 NAG.6: 2 residues within 4Å: Chain A: E.190, N.192 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.190 NAG.7: 3 residues within 4Å: Chain A: N.215, T.217, T.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 NAG.8: 3 residues within 4Å: Chain A: M.253, N.266, T.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.266, A:T.268 NAG.9: 6 residues within 4Å: Chain A: T.268, Q.269, N.272, T.274, C.275, C.284 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: N.159, G.160, L.162, N.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial. Mbio (2020)

Release Date

2019-09-25

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
M48U1 CD4 mimetic peptide: B
CH54 Fab heavy chain: C
CH54 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
N

C
H

D
L

clade A/E 93TH057 HIV-1 gp120 core

M48U1 CD4 mimetic peptide

CH54 Fab heavy chain

CH54 Fab light chain

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