SMTL ID : 5w4l.1 (1 other biounit)

Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.58 No protein-ligand interaction detected (PLIP) NAG.2: 5 residues within 4Å: Chain A: N.131, T.133, P.135, I.169, H.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.131 NAG.3: 4 residues within 4Å: Chain A: H.55, N.126, N.138 Chain F: S.31 No protein-ligand interaction detected (PLIP) NAG.4: 8 residues within 4Å: Chain A: D.108, P.109, K.149, L.158, N.159, C.319, V.320, S.321 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.158 Hydrogen bonds: A:D.108, A:K.149, A:S.321 NAG.5: 3 residues within 4Å: Chain A: N.173, T.175, N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.173, A:T.175 NAG.6: 6 residues within 4Å: Chain A: E.165, E.166, I.167, N.186, Q.225, K.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.167 NAG.7: 2 residues within 4Å: Chain A: N.192, E.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.192, A:E.213 NAG.8: 3 residues within 4Å: Chain A: N.215, T.217, K.218 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.252, M.253, N.266, T.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.266 NAG.10: 7 residues within 4Å: Chain A: T.268, Q.269, N.272, T.274, K.282, G.283, C.284 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.268 Hydrogen bonds: A:N.272, A:K.282, A:C.284 NAG.11: 6 residues within 4Å: Chain A: G.160, L.162, S.188, E.190, N.322, T.324 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.324 Hydrogen bonds: A:S.188, A:N.322

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain A: G.247 Chain B: R.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region. Structure (2017)

Release Date

2017-11-15

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
CD4 mimetic peptide M48U1: B
Antibody N5-i5 Fab heavy chain: C
Antibody N5-i5 light chain: D
Antibody N12-i3 Fab heavy chain: E
Antibody N12-i3 light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
N

C
H

D
L

E
D

F
E

clade A/E 93TH057 HIV-1 gp120 core

CD4 mimetic peptide M48U1

Antibody N5-i5 Fab heavy chain

Antibody N5-i5 light chain

Antibody N12-i3 Fab heavy chain

Antibody N12-i3 light chain

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