SMTL ID : 6opn.1

CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: V.90, N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: V.90, N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain G: V.90, N.245, N.257 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 17 residues within 4Å: Chain A: V.224, S.225, F.226, E.227, R.268, N.278, N.391, C.392, G.393, I.450, R.451, G.452, Q.453, I.454, S.457, S.458 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.227, A:G.452 NAG-NAG-BMA-MAN-MAN.4: 17 residues within 4Å: Chain D: V.224, S.225, F.226, E.227, R.268, N.278, N.391, C.392, G.393, I.450, R.451, G.452, Q.453, I.454, S.457, S.458 Ligands: NAG.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.227, D:G.452 NAG-NAG-BMA-MAN-MAN.6: 17 residues within 4Å: Chain G: V.224, S.225, F.226, E.227, R.268, N.278, N.391, C.392, G.393, I.450, R.451, G.452, Q.453, I.454, S.457, S.458 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.227, G:G.452

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

NAG.7: 4 residues within 4Å: Chain A: N.250, G.253, S.290, E.291 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.292, T.294, D.295 Ligand excluded by PLIP NAG.9: 8 residues within 4Å: Chain A: E.309, N.311, N.347, I.348, S.349, N.424, R.455 Ligands: NAG.14 Ligand excluded by PLIP NAG.10: 7 residues within 4Å: Chain A: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG.14 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: I.374, F.375, N.376, N.406 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: T.387, N.400, T.402 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: P.403, N.406 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: Q.423, N.424 Ligands: NAG.9, NAG.10 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain D: N.250, G.253, S.290, E.291 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain D: N.292, T.294, D.295 Ligand excluded by PLIP NAG.19: 8 residues within 4Å: Chain D: E.309, N.311, N.347, I.348, S.349, N.424, R.455 Ligands: NAG.24 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain D: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG.24 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: I.374, F.375, N.376, N.406 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: T.387, N.400, T.402 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: P.403, N.406 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain D: Q.423, N.424 Ligands: NAG.19, NAG.20 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain G: N.250, G.253, S.290, E.291 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain G: N.292, T.294, D.295 Ligand excluded by PLIP NAG.29: 8 residues within 4Å: Chain G: E.309, N.311, N.347, I.348, S.349, N.424, R.455 Ligands: NAG.34 Ligand excluded by PLIP NAG.30: 7 residues within 4Å: Chain G: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG.34 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: I.374, F.375, N.376, N.406 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: T.387, N.400, T.402 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: P.403, N.406 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain G: Q.423, N.424 Ligands: NAG.29, NAG.30 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain G: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.6 Ligand excluded by PLIP

3 x N07: [3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methanone(Non-covalent)

N07.16: 8 residues within 4Å: Chain B: I.8, F.11, L.26, T.27, A.30, Y.75 Chain E: Q.80, L.81 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:F.11, B:L.26, B:Y.75, E:Q.80, E:L.81 pi-Stacking: B:F.11 N07.26: 8 residues within 4Å: Chain E: I.8, F.11, L.26, T.27, A.30, Y.75 Chain H: Q.80, L.81 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:F.11, E:L.26, E:Y.75, H:Q.80, H:L.81 pi-Stacking: E:F.11 N07.36: 8 residues within 4Å: Chain B: Q.80, L.81 Chain H: I.8, F.11, L.26, T.27, A.30, Y.75 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: H:F.11, H:L.26, H:Y.75, B:Q.80, B:L.81 pi-Stacking: H:F.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozorowski, G. et al., A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Cell Rep (2020)

Release Date

2020-10-21

Peptides

Envelope glycoprotein gp160: ADG
Envelope glycoprotein gp41: BEH
T-cell surface glycoprotein CD4: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

B
B

E
E

H
H

C
C

F
F

I
I

Envelope glycoprotein gp160

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

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