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

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

Coordinates

PDB Format Compare

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: 5 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, H.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:T.120 Water bridges: A:T.120 NAG.2: 3 residues within 4Å: Chain A: D.114, K.115, N.125 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.114 Hydrogen bonds: A:D.114, A:K.115, A:N.125 NAG.3: 10 residues within 4Å: Chain A: D.95, P.96, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 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 Water bridges: A:N.163 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:I.154, A:I.154, A:N.173 NAG.6: 4 residues within 4Å: Chain A: N.179, Y.198, E.200, V.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.179, A:E.200, A:E.200 Water bridges: A:T.181, A:N.305 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 Water bridges: A:K.205 NAG.8: 4 residues within 4Å: Chain A: K.218, E.219, N.222, N.223 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.223 Water bridges: A:N.222, A:N.223 NAG.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 5 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.255, A:Q.256 NAG.11: 6 residues within 4Å: Chain A: K.136, N.146, L.149, S.175, N.309 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 Water bridges: A:S.175, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: 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: 15 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:F.249, A:W.288 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
A

clade A/E 93TH057 HIV-1 gp120 core

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