SMTL ID : 7n6w.1

Structure of uncleaved HIV-1 JR-FL Env glycoprotein trimer in state U2 bound to small Molecule HIV-1 Entry Inhibitor BMS-378806

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: K.132, N.154, Y.171 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: V.85, E.87, N.227, N.239 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain A: N.293, N.329, T.405 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain A: N.358, I.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain A: N.382, T.384 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: E.87, N.88, S.520 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain B: N.299, E.318, I.320 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain B: N.329, T.407 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain B: N.358, I.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 2 residues within 4Å: Chain B: N.382, T.384 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain C: N.154, Y.171, L.173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 4 residues within 4Å: Chain C: N.293, H.327, N.329 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 3 residues within 4Å: Chain C: M.369, N.382, T.384 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 3 residues within 4Å: Chain C: T.384, Q.385, N.388 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.158, K.169 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.274, T.276, N.277 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.277 NAG-NAG.6: 4 residues within 4Å: Chain A: E.291, N.293, N.329 Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.299, I.320 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: R.332, N.336, K.340, W.391 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.388 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: V.134, N.154, K.169, Y.171, L.173 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.169 NAG-NAG.16: 2 residues within 4Å: Chain B: N.158, Q.168 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: V.85, N.227, K.229, N.239 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.85 NAG-NAG.19: 4 residues within 4Å: Chain B: E.291, N.293, R.436 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain B: N.388 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: R.250, N.440 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain B: N.603, S.605 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: R.625, E.626, N.629 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.158, V.167, K.169 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: N.293 Ligands: NAG-NAG-BMA.34 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain C: N.299, I.320 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain C: N.358, R.461 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 2 residues within 4Å: Chain C: N.603, S.605 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 1 residues within 4Å: Chain C: N.629 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN.4: 13 residues within 4Å: Chain A: S.207, E.209, P.210, R.250, N.260, N.373, C.374, G.375, I.431, R.436, C.437, S.438, S.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.375, A:S.438 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 17 residues within 4Å: Chain B: E.64, S.207, R.250, L.259, N.260, R.302, N.373, C.374, I.431, R.432, G.433, I.435, R.436, C.437, S.438, S.439 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.13: 2 residues within 4Å: Chain A: N.260, N.440 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.38: 4 residues within 4Å: Chain C: R.250, E.291, N.440 Ligands: NAG-NAG-BMA-MAN-MAN.31 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.30: 2 residues within 4Å: Chain C: N.227, N.239 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-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.31: 8 residues within 4Å: Chain C: P.210, R.250, V.252, N.260, N.373, C.374, S.438 Ligands: NAG-NAG-BMA-MAN.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.438

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

NAG.41: 2 residues within 4Å: Chain A: E.87, N.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.87 Hydrogen bonds: A:E.87 NAG.42: 2 residues within 4Å: Chain A: V.134, N.135 No protein-ligand interaction detected (PLIP) NAG.43: 1 residues within 4Å: Chain A: N.629 No protein-ligand interaction detected (PLIP) NAG.45: 1 residues within 4Å: Chain B: N.608 No protein-ligand interaction detected (PLIP) NAG.46: 1 residues within 4Å: Chain B: N.617 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.617 NAG.48: 3 residues within 4Å: Chain C: R.347, N.352, N.393 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.393 Hydrogen bonds: C:N.352 NAG.49: 1 residues within 4Å: Chain C: N.617 No protein-ligand interaction detected (PLIP)

3 x 83G: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione(Non-covalent)

83G.44: 14 residues within 4Å: Chain A: I.109, W.112, D.113, L.116, V.253, S.371, F.378, I.416, N.417, M.418, W.419, K.424, A.425, M.467 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.112, A:V.253, A:F.378, A:F.378, A:W.419 Hydrogen bonds: A:W.419, A:Q.420, A:K.424 83G.47: 14 residues within 4Å: Chain B: I.109, W.112, V.253, S.371, N.373, F.378, Y.380, I.416, N.417, M.418, W.419, K.424, M.426, M.467 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.112, B:V.253, B:F.378, B:F.378, B:I.416, B:W.419, B:W.419, B:M.426 Hydrogen bonds: B:W.419 83G.50: 16 residues within 4Å: Chain C: I.109, W.112, D.113, V.252, V.253, S.254, E.366, S.371, N.373, I.416, N.417, M.418, W.419, K.424, A.425, M.426 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.112, C:V.253, C:V.253, C:M.426 pi-Stacking: C:W.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Asymmetric Structures and Conformational Plasticity of the Uncleaved Full-Length Human Immunodeficiency Virus Envelope Glycoprotein Trimer. J.Virol. (2021)

Release Date

2021-09-22

Peptides

Envelope glycoprotein gp160: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Envelope glycoprotein gp160

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