SMTL ID : 6ut1.1

CRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH BNM-III-170

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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.120, T.122, P.124, I.158, S.160, H.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.120 NAG.2: 4 residues within 4Å: Chain A: H.44, N.115, K.117, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115, A:K.117, A:N.127 NAG.3: 9 residues within 4Å: Chain A: D.97, K.138, L.147, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:D.97, A:S.310 Water bridges: A:D.97 NAG.4: 3 residues within 4Å: Chain A: N.162, T.164, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.162, A:N.165 NAG.5: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, K.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.156, A:Q.214, A:K.218, A:K.218 NAG.6: 4 residues within 4Å: Chain A: N.181, Y.200, E.202, N.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.181, A:Y.200 NAG.7: 3 residues within 4Å: Chain A: N.204, K.207, T.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 NAG.8: 4 residues within 4Å: Chain A: T.241, M.242, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.9: 2 residues within 4Å: Chain A: N.224, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 NAG.10: 4 residues within 4Å: Chain A: L.151, S.177, N.311 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.177, A:N.311

1 x 5VG: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide(Non-covalent)

5VG.11: 17 residues within 4Å: Chain A: V.141, S.142, T.143, E.239, I.240, S.244, F.245, N.246, F.251, N.288, M.289, W.290, G.292, G.335, G.336, D.337, M.338 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.143, A:I.240 Hydrogen bonds: A:N.288, A:M.289, A:G.335, A:G.336 pi-Stacking: A:W.290 Halogen bonds: A:S.244

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

EPE.12: 6 residues within 4Å: Chain A: L.11, C.13, H.31, A.32, Q.62, D.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.62, A:Q.62 Salt bridges: A:D.66, A:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prevost, J. et al., The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site. Mbio (2020)

Release Date

2020-10-07

Peptides

HIV-1 LM/HS clade A/E CRF01 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 LM/HS clade A/E CRF01 gp120 core

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