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

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.118, T.120, P.122, S.158 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: H.42, N.113, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.113, A:N.125 NAG.3: 6 residues within 4Å: Chain A: L.145, N.146, 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:S.308 Water bridges: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:I.154, A:N.173 NAG.6: 2 residues within 4Å: Chain A: N.179, E.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:E.200 Water bridges: A:T.181, A:N.305 NAG.7: 4 residues within 4Å: Chain A: N.202, K.205, G.273, T.274 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: E.219, N.222, N.223 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:T.239, A:T.255 NAG.10: 4 residues within 4Å: Chain A: Q.229, P.230, T.255, N.259 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.255 Hydrogen bonds: A:N.259 NAG.11: 5 residues within 4Å: Chain A: K.136, N.146, 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 0LY: N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide(Non-covalent)

0LY.12: 16 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, Q.289, G.290, G.334, N.335 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.139, A:T.141, A:F.249, A:I.285 Hydrogen bonds: A:N.286, A:G.334 pi-Stacking: A:W.288

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

EPE.13: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.64, A:D.64

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

Related Entries With Identical Sequence