SMTL ID : 4dvv.2 (1 other biounit)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-I-261

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, I.156, 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: E.40, N.113, K.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:K.115, A:N.125 NAG.3: 11 residues within 4Å: Chain A: D.95, P.96, K.136, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:R.246 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160, A:T.162 NAG.5: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:N.173 NAG.6: 6 residues within 4Å: Chain A: E.177, N.179, T.181, Y.198, E.200, V.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:E.200 Water bridges: A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: E.219, N.222, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.9: 2 residues within 4Å: Chain A: N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:T.255, A:T.255 NAG.10: 3 residues within 4Å: Chain A: T.255, N.259, T.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.255 Hydrogen bonds: A:N.259, A:T.261 NAG.11: 3 residues within 4Å: Chain A: N.146, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.9 Water bridges: A:Q.60 Salt bridges: A:D.64, A:D.64

1 x 0M1: N-{[(4S,5S)-5-(aminomethyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl}-N'-(4-chloro-3-fluorophenyl)ethanediamide(Non-covalent)

0M1.13: 16 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, I.238, S.242, F.243, N.244, F.249, N.286, M.287, W.288, G.333, G.334, N.335 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:F.249 Hydrogen bonds: A:D.235, A:N.286, A:G.333, A:G.334 pi-Stacking: A:W.288

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

clade A/E 93TH057 HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

clade A/E 93TH057 HIV-1 gp120 core

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