SMTL ID : 6w4m.1

CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48U1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, S.158, L.161, H.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:H.220 NAG.2: 3 residues within 4Å: Chain A: H.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113 NAG.3: 9 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, N.146, R.246, C.306, V.307, S.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.138 Hydrogen bonds: A:N.146, A:R.246, A:S.308 NAG.4: 2 residues within 4Å: Chain A: N.160, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:Q.212 NAG.6: 6 residues within 4Å: Chain A: N.179, T.181, Y.198, K.303, N.305, V.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:K.205 NAG.8: 4 residues within 4Å: Chain A: L.236, M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.236 Hydrogen bonds: A:N.253, A:T.255 NAG.9: 6 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, K.269, G.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.261, A:G.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site. Bmc Biol. (2020)

Release Date

2020-08-05

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN: B
ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN: C
M48U1 CD4 MIMETIC PEPTIDE: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
L

C
H

D
N

clade A/E 93TH057 HIV-1 gp120 core

ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN

ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN

M48U1 CD4 MIMETIC PEPTIDE

Related Entries With Identical Sequence