SMTL ID : 4dvr.1

Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.79, T.81, S.119, F.122 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:N.79 NAG.2: 8 residues within 4Å: Chain A: P.57, R.97, L.106, N.107, C.266, S.267, S.268 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.106 Hydrogen bonds: A:N.107, A:S.268 NAG.3: 3 residues within 4Å: Chain A: N.121, T.123, N.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.121, A:T.123 NAG.4: 4 residues within 4Å: Chain A: E.113, N.134, E.135, Q.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113 Water bridges: A:E.114 NAG.5: 3 residues within 4Å: Chain A: N.140, N.161, R.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.265 NAG.6: 2 residues within 4Å: Chain A: N.215, T.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.215, A:R.240 NAG.7: 4 residues within 4Å: Chain A: R.97, S.136, N.269 Ligands: NAG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.97, A:R.97, A:S.136, A:S.136

1 x 0LY: N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide(Non-covalent)

0LY.8: 17 residues within 4Å: Chain A: V.100, S.101, T.102, E.199, S.204, F.205, N.206, F.211, I.245, N.246, M.247, W.248, E.250, V.251, G.294, D.295, M.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.102, A:E.199, A:E.199, A:V.251 Hydrogen bonds: A:N.246, A:G.294 pi-Stacking: A:W.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, Y.D. et al., Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site. Plos One (2014)

Release Date

2013-02-27

Peptides

Envelope glycoprotein gp120: A
Fab 48d Light chain: B
Fab 48d Heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
L

C
H

Envelope glycoprotein gp120

Fab 48d Light chain

Fab 48d Heavy chain

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