SMTL ID : 5kjr.1

Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 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: 4 residues within 4Å: Chain A: N.118, S.158, L.161, H.220 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.161 NAG.2: 4 residues within 4Å: Chain A: H.42, N.113, K.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.42, A:K.115, A:K.115 NAG.3: 9 residues within 4Å: Chain A: D.95, K.136, V.138, L.145, N.146, N.244, C.306, V.307, S.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.160, A:T.162, A:T.162, A:N.163 NAG.5: 6 residues within 4Å: Chain A: E.153, I.154, N.173, K.174, Q.212, K.216 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.174 Hydrogen bonds: A:E.153, A:E.153, A:I.154, A:Q.212 NAG.6: 4 residues within 4Å: Chain A: N.179, E.200, N.305, V.307 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:T.204, A:K.205 NAG.8: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.239 Hydrogen bonds: A:N.253, A:T.255 NAG.9: 4 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.261, A:C.262 NAG.10: 1 residues within 4Å: Chain A: N.322 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.11: 5 residues within 4Å: Chain C: G.44 Chain D: D.92, Y.94, G.108, K.111 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.111 Hydrogen bonds: D:G.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, S. et al., A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability. J.Virol. (2016)

Release Date

2016-07-20

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
M48U1 CD4 MIMETIC PEPTIDE: B
N60-I3 FAB HEAVY CHAIN: C
N60-I3 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

N60-I3 FAB HEAVY CHAIN

N60-I3 FAB LIGHT CHAIN

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