SMTL ID : 8gdk.1

Crystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-151

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.120, T.122, I.158, S.160, H.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.158 Hydrogen bonds: A:N.120, A:H.222 NAG.2: 2 residues within 4Å: Chain A: N.115, N.127 No protein-ligand interaction detected (PLIP) NAG.3: 7 residues within 4Å: Chain A: P.98, K.138, N.148, N.246, C.308, V.309, S.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.138, A:N.148, A:S.310 NAG.4: 4 residues within 4Å: Chain A: N.162, T.164, N.165 Ligands: NAG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.162, A:T.164 NAG.5: 7 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.176, Q.214, K.218 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.176 Hydrogen bonds: A:I.156, A:Q.214, A:Q.214 NAG.6: 5 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:Y.200 NAG.7: 5 residues within 4Å: Chain A: N.204, T.206, K.207, G.275, T.276 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.276 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 NAG.10: 4 residues within 4Å: Chain A: N.148, L.151, S.177, N.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.177, A:N.311 NAG.11: 3 residues within 4Å: Chain A: P.232, T.257, N.261 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: T.164, N.324 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain A: N.274 No protein-ligand interaction detected (PLIP)

1 x Z7N: (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-1-carbonyl]piperidine-3-carboxamide(Non-covalent)

Z7N.14: 16 residues within 4Å: Chain A: V.141, S.142, T.143, D.237, E.239, T.244, F.245, F.251, I.287, N.288, M.289, W.290, G.292, G.336, D.337, M.338 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:E.239, A:F.251, A:I.287, A:N.288, A:D.337 Hydrogen bonds: A:D.237, A:D.237, A:N.288 pi-Stacking: A:W.290 Halogen bonds: A:T.244

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

EPE.15: 7 residues within 4Å: Chain A: L.11, C.13, H.31, A.32, Q.62, D.66, Y.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.11 Salt bridges: A:D.66, A:D.66

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: M.297 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Crystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-151. To Be Published

Release Date

2024-03-20

Peptides

HIV-1 LM/HT Clade A/E CRF01 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 LM/HT Clade A/E CRF01 gp120 core

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