SMTL ID : 6x5c.1

Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 14 residues within 4Å: Chain A: S.225, E.227, P.228, V.270, L.277, N.278, C.392, G.393, I.450, R.451, G.452, S.457, S.458 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.451 NAG-NAG-BMA-MAN-MAN.2: 16 residues within 4Å: Chain D: S.225, E.227, P.228, V.270, N.278, N.391, C.392, G.393, I.450, R.451, G.452, Q.453, R.455, C.456, S.458 Ligands: NAG.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.451, D:Q.453 NAG-NAG-BMA-MAN-MAN.4: 13 residues within 4Å: Chain G: S.225, P.228, V.270, L.277, N.278, C.392, G.393, I.450, R.451, G.452, S.457, S.458 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.451

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

NAG-NAG.3: 5 residues within 4Å: Chain G: E.88, V.90, G.92, N.245, N.257 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:E.88

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

NAG.5: 4 residues within 4Å: Chain A: V.90, G.92, T.256, N.257 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.292 Ligands: NAG.13 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: E.309, N.311, N.347, R.455 Ligand excluded by PLIP NAG.8: 7 residues within 4Å: Chain A: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG.11 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: F.375, N.376, N.406, R.480 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: Q.423, N.424 Ligands: NAG.8 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: N.278, S.457, S.458, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP NAG.13: 7 residues within 4Å: Chain A: N.250, S.252, S.290, E.291, N.292, I.293 Ligands: NAG.6 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain D: V.90, G.92, T.256, N.257 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain D: N.292 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain D: E.309, N.311, N.347 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: N.311, T.313, H.345, N.347 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: N.376, H.377, F.405, N.406 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain D: H.377, V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: Q.423, N.424 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain D: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain G: N.292, I.293, T.294 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain G: E.309, N.311, N.347, R.455 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain G: H.345, N.347, N.424, T.426 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain G: H.377, V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain G: P.403, N.406, I.425 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: N.278, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP

3 x UOV: N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide(Non-covalent)

UOV.14: 17 residues within 4Å: Chain B: A.6, F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91, I.92 Chain H: E.73, L.76, R.77, Q.80, L.81, G.83, I.84 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain H Hydrophobic interactions: B:A.6, B:F.7, B:F.7, B:F.7, B:V.72, B:Y.75, B:Y.75, B:I.92, H:L.76, H:R.77, H:Q.80, H:Q.80, H:L.81 pi-Stacking: B:F.11 UOV.23: 15 residues within 4Å: Chain B: E.73, L.76, R.77, Q.80, L.81 Chain E: A.6, F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91, I.92 13 PLIP interactions: 8 interactions with chain E, 5 interactions with chain B Hydrophobic interactions: E:F.7, E:F.7, E:F.7, E:V.72, E:Y.75, E:Y.75, E:I.92, B:E.73, B:L.76, B:R.77, B:Q.80, B:L.81 pi-Stacking: E:F.11 UOV.30: 14 residues within 4Å: Chain E: E.73, L.76, R.77, Q.80, L.81, I.84 Chain H: F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain H Hydrophobic interactions: E:L.76, E:L.76, E:R.77, E:Q.80, H:F.7, H:F.7, H:F.11, H:V.72, H:I.91 pi-Stacking: H:Y.75

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
E

B
B

E
F

H
G

C
C

F
I

I
J

Envelope glycoprotein gp160

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

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