SMTL ID : 6usw.1

CRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH (S)-MCG-IV-210

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.120, T.122, G.123, P.124, I.158, L.163, H.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120, A:H.222 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.127 NAG.3: 11 residues within 4Å: Chain A: D.97, P.98, K.138, L.147, N.148, N.246, R.248, C.308, V.309, S.310 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:K.138, A:N.148, A:R.248, A:R.248, A:S.310 NAG.4: 3 residues within 4Å: Chain A: N.162, T.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 NAG.5: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, K.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.156, A:K.218, A:K.218 NAG.6: 5 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, V.309 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.181, A:T.183, A:Y.200 NAG.7: 3 residues within 4Å: Chain A: N.204, K.207, T.276 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.276 Hydrogen bonds: A:N.204 NAG.8: 3 residues within 4Å: Chain A: T.241, N.255, T.257 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.225 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: N.148, 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 O51: (3S)-N~1~-(2-aminoethyl)-N~3~-(4-chloro-3-fluorophenyl)piperidine-1,3-dicarboxamide(Non-covalent)

O51.11: 14 residues within 4Å: Chain A: V.141, S.142, T.143, E.239, S.244, F.245, N.246, F.251, N.288, M.289, W.290, G.335, G.336, D.337 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.251, A:N.288 Hydrogen bonds: A:N.288, A:G.335, A:G.336, A:D.337 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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