SMTL ID : 9jkg.1

Asymmetric structure of cleaved HIV-1 Tri FPPR envelope glycoprotein trimer in amphipol-lipid nanodiscs (Tri FPPR.2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

26 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: 2 residues within 4Å: Chain A: N.610, S.612 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: R.632, N.636 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain B: V.179, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.273, T.275, D.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 2 residues within 4Å: Chain B: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain B: N.388 Ligands: NAG-NAG-BMA-MAN.18, NAG-NAG-BMA-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: S.288, S.443, N.445 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain C: R.632, E.633, D.635, N.636 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 3 residues within 4Å: Chain D: N.88 Chain F: G.526, S.527 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 2 residues within 4Å: Chain D: N.157 Ligands: NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 1 residues within 4Å: Chain D: N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 3 residues within 4Å: Chain D: D.227, K.228, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 5 residues within 4Å: Chain D: E.290, N.292, N.328, T.410 Ligands: NAG-NAG-BMA-MAN.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 2 residues within 4Å: Chain D: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 2 residues within 4Å: Chain D: N.382, T.384 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 1 residues within 4Å: Chain D: N.388 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 5 residues within 4Å: Chain D: R.249, N.259, S.443, N.445 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.44: 4 residues within 4Å: Chain E: N.153, Y.170, G.316, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.45: 2 residues within 4Å: Chain E: N.157, K.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 3 residues within 4Å: Chain D: H.305 Chain E: I.181, N.194 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.183 NAG-NAG-BMA.47: 3 residues within 4Å: Chain E: N.231, F.274, Q.348 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.48: 3 residues within 4Å: Chain E: D.227, K.228, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.51: 5 residues within 4Å: Chain E: N.292, N.328, I.329, T.410 Ligands: NAG-NAG-BMA-MAN-MAN.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.55: 2 residues within 4Å: Chain E: V.356, N.358 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.57: 1 residues within 4Å: Chain E: N.388 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.58: 4 residues within 4Å: Chain E: N.259, S.288, E.290, N.445 No protein-ligand interaction detected (PLIP)

10 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: 1 residues within 4Å: Chain A: N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: E.87, N.88 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.183, D.184, N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.231, G.234, P.235, F.274, Q.348 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: K.228, N.238, E.265 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.292, N.328 Ligands: NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain C: N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 1 residues within 4Å: Chain D: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain A: S.527 Chain E: E.87, N.88 No protein-ligand interaction detected (PLIP) NAG-NAG.61: 1 residues within 4Å: Chain F: N.624 No protein-ligand interaction detected (PLIP)

4 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.5: 3 residues within 4Å: Chain B: N.130, T.186 Ligands: NAG.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.29: 7 residues within 4Å: Chain B: I.162 Chain D: P.180, I.181, D.182, R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.36: 4 residues within 4Å: Chain D: N.292, N.328, T.410 Ligands: NAG-NAG-BMA.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.52: 1 residues within 4Å: Chain E: N.298 No protein-ligand interaction detected (PLIP)

7 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.6: 3 residues within 4Å: Chain B: D.133, N.153, Y.170 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.170 NAG-NAG-BMA-MAN.15: 6 residues within 4Å: Chain B: N.292, H.326, N.328, T.410, T.412 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 4 residues within 4Å: Chain B: N.382, T.384, R.416 Ligands: NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.33: 3 residues within 4Å: Chain D: N.273, T.275, D.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.38: 1 residues within 4Å: Chain D: N.358 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.50: 2 residues within 4Å: Chain E: N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.56: 3 residues within 4Å: Chain E: M.369, N.382, T.384 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.11: 13 residues within 4Å: Chain B: H.66, S.206, E.208, P.209, R.249, V.251, N.259, R.301, I.436, R.441, C.442, S.444 Ligands: NAG-NAG-BMA.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.208, B:E.208 NAG-NAG-BMA-MAN-MAN-MAN.49: 10 residues within 4Å: Chain E: S.206, E.208, V.251, N.259, F.372, N.373, G.375, R.437, C.442, S.444 No protein-ligand interaction detected (PLIP)

5 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.16: 9 residues within 4Å: Chain B: N.335, T.390, N.392, N.394, G.395, T.396, W.397, L.399, T.400 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.397 Hydrogen bonds: B:T.396, B:T.396, B:T.396 NAG-NAG-BMA-MAN-MAN.25: 3 residues within 4Å: Chain D: N.130, T.186 Ligands: NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 6 residues within 4Å: Chain D: R.135, N.153, S.155, K.168, Y.170, D.317 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.168 NAG-NAG-BMA-MAN-MAN.43: 3 residues within 4Å: Chain E: N.130, T.132, T.186 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.53: 5 residues within 4Å: Chain E: N.292, H.326, N.328, T.410 Ligands: NAG-NAG-BMA.51 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- BMA: 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-MAN-BMA.17: 5 residues within 4Å: Chain B: N.358, Q.359, F.387, N.388, R.467 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.21: 2 residues within 4Å: Chain C: N.610, S.612 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.59: 2 residues within 4Å: Chain F: N.610, S.612 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.32: 12 residues within 4Å: Chain D: V.65, E.208, P.209, R.249, V.251, N.259, N.373, R.441, C.442, S.443, S.444 Ligands: NAG-NAG-BMA.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.208, D:S.443

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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.37: 7 residues within 4Å: Chain D: R.331, N.335, N.394, G.395, T.396, W.397, T.400 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.397 Hydrogen bonds: D:T.396, D:T.396 NAG-NAG-BMA-MAN-MAN-MAN-MAN.54: 7 residues within 4Å: Chain E: N.335, N.339, W.391, N.394, G.395, T.396, T.400 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.396

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.60: 2 residues within 4Å: Chain F: N.615, M.620 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.62: 3 residues within 4Å: Chain F: R.632, E.633, N.636 No protein-ligand interaction detected (PLIP)

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

NAG.63: 2 residues within 4Å: Chain A: N.623, N.624 No protein-ligand interaction detected (PLIP) NAG.65: 6 residues within 4Å: Chain B: N.130, S.155, F.156, N.157, K.168 Ligands: NAG-NAG-BMA-MAN.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.130 Hydrogen bonds: B:N.130, B:N.157 NAG.66: 2 residues within 4Å: Chain B: N.351, N.352 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.351, B:N.352 NAG.67: 2 residues within 4Å: Chain B: F.393, N.394 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.394 NAG.68: 2 residues within 4Å: Chain B: T.396, N.398 No protein-ligand interaction detected (PLIP) NAG.69: 1 residues within 4Å: Chain C: N.624 No protein-ligand interaction detected (PLIP) NAG.71: 1 residues within 4Å: Chain D: N.352 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.352 NAG.72: 1 residues within 4Å: Chain D: N.398 No protein-ligand interaction detected (PLIP) NAG.74: 3 residues within 4Å: Chain E: N.183, D.184, N.185 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.185 NAG.75: 3 residues within 4Å: Chain E: G.350, N.351, N.352 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.351, E:N.352 NAG.76: 1 residues within 4Å: Chain E: N.398 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.398

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.64: 14 residues within 4Å: Chain B: I.109, W.112, D.113, L.116, V.252, S.371, F.378, I.421, N.422, M.423, W.424, K.429, M.431, M.473 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.112, B:L.116, B:V.252, B:F.378, B:W.424 Hydrogen bonds: B:D.113, B:W.424 pi-Stacking: B:W.424 83G.70: 15 residues within 4Å: Chain D: I.109, W.112, D.113, L.116, V.252, S.371, F.372, N.373, F.378, I.421, N.422, M.423, W.424, K.429, M.431 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.112, D:W.112, D:L.116, D:V.252, D:I.421, D:I.421, D:I.421, D:M.431 Hydrogen bonds: D:D.113, D:W.424 pi-Stacking: D:W.424 83G.73: 13 residues within 4Å: Chain E: I.109, W.112, L.116, V.252, S.371, F.378, I.421, N.422, M.423, W.424, K.429, M.431, M.473 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:W.112, E:L.116, E:V.252, E:F.378, E:F.378, E:I.421, E:W.424 Hydrogen bonds: E:W.424 pi-Stacking: E:W.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qi, Y. et al., The membrane-proximal external region of human immunodeficiency virus (HIV-1) envelope glycoprotein trimers in A18-lipid nanodiscs. Commun Biol (2025)

Release Date

2025-02-26

Peptides

Envelope glycoprotein gp160: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
A

F
F

Envelope glycoprotein gp160

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