SMTL ID : 6ofi.1

CRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.46, N.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47 NAG.2: 6 residues within 4Å: Chain A: N.120, T.122, P.124, I.158, S.160, L.163 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.3: 4 residues within 4Å: Chain A: H.44, N.115, K.117, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.44, A:K.117, A:K.117 NAG.4: 8 residues within 4Å: Chain A: P.98, V.140, L.147, N.148, R.248, C.308, V.309, S.310 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.140, A:L.147 Hydrogen bonds: A:N.148, A:R.248 NAG.5: 5 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.156, A:N.175, A:Q.214 NAG.6: 2 residues within 4Å: Chain A: N.181, V.309 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.181 NAG.7: 3 residues within 4Å: Chain A: N.204, K.207, T.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204, A:K.207 NAG.8: 3 residues within 4Å: Chain A: M.242, N.255, T.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.255, A:T.257 NAG.9: 6 residues within 4Å: Chain A: T.257, Q.258, N.261, T.263, C.264, C.273 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: G.149, N.311 No protein-ligand interaction detected (PLIP)

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

2020-06-24

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
CH55 Fab heavy chain: B
CH55 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

CH55 Fab heavy chain

CH55 Fab light chain

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