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

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with MAE-II-167

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, P.122, I.156, S.158, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.120 Water bridges: A:N.118 NAG.2: 3 residues within 4Å: Chain A: K.115, K.124, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.115, A:K.115 NAG.3: 7 residues within 4Å: Chain A: L.145, N.146, N.244, C.306, V.307, S.308 Ligands: NAG.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:S.308 Water bridges: A:K.136, A:V.307 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: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:I.154, A:N.173 Water bridges: A:N.173, A:Q.212 NAG.6: 4 residues within 4Å: Chain A: N.179, Y.198, E.200, V.307 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:Y.198, A:Y.198 Water bridges: A:T.181 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.8: 4 residues within 4Å: Chain A: K.218, E.219, N.222, N.223 1 PLIP interactions: 1 interactions with chain A Water bridges: 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: K.136, N.146, S.175, N.309 Ligands: NAG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.136, 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.11: 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 0M4: N-(4-chloro-3-fluorophenyl)-N'-[(3aS,6aS)-hexahydrocyclopenta[c]pyrrol-3a(1H)-ylmethyl]ethanediamide(Non-covalent)

0M4.12: 17 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, I.285, N.286, M.287, W.288, G.333, G.334, N.335 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:I.238, A:F.249, A:I.285, A:W.288 Hydrogen bonds: A:D.235, A:N.286, 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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