SMTL ID : 9jkf.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

29 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.4: 3 residues within 4Å: Chain A: R.632, E.633, N.636 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain B: E.87, N.88 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain B: N.130 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain B: D.133, N.136, N.153, Y.170, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain B: V.179, N.194, T.195 Chain E: H.305 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain B: N.231, T.233, P.235, S.272 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.235 NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: K.228, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain B: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: N.382, T.384, R.416 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain B: Q.359, N.388 Ligands: NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain B: S.288, S.443, N.445 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 2 residues within 4Å: Chain C: D.635, N.636 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain D: E.87, N.88 Chain F: S.527 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 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.35: 4 residues within 4Å: Chain D: D.227, K.228, K.237, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 3 residues within 4Å: Chain D: N.273, T.275, D.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 4 residues within 4Å: Chain D: N.292, N.328, S.443 Ligands: NAG-NAG-BMA-MAN.40 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 2 residues within 4Å: Chain D: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 3 residues within 4Å: Chain D: N.382, T.384 Ligands: NAG-NAG-BMA-MAN.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 5 residues within 4Å: Chain D: N.259, E.290, S.443, N.445 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 3 residues within 4Å: Chain A: S.527 Chain E: E.87, N.88 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.50: 5 residues within 4Å: Chain E: T.128, N.157, K.168 Ligands: NAG-NAG-BMA-MAN-MAN.48, NAG-NAG-BMA-MAN-MAN.48 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.52: 5 residues within 4Å: Chain D: H.305 Chain E: V.179, P.180, I.181, N.194 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.179 NAG-NAG-BMA.54: 3 residues within 4Å: Chain E: D.227, K.228, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.57: 2 residues within 4Å: Chain E: N.292, N.328 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.58: 2 residues within 4Å: Chain E: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.61: 3 residues within 4Å: Chain E: V.356, N.358, R.467 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.65: 6 residues within 4Å: Chain E: N.259, S.288, E.290, S.443, N.445 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.55 No protein-ligand interaction detected (PLIP)

16 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.3: 1 residues within 4Å: Chain A: N.624 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.130, N.157 Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.292, N.328 Ligands: NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain B: W.397, N.398 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.624, M.625, E.629 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 2 residues within 4Å: Chain D: T.128, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain D: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain D: N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 3 residues within 4Å: Chain E: N.183, D.184, N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 4 residues within 4Å: Chain E: N.231, P.235, F.274, Q.348 No protein-ligand interaction detected (PLIP) NAG-NAG.64: 4 residues within 4Å: Chain E: T.396, W.397, N.398 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.60 No protein-ligand interaction detected (PLIP) NAG-NAG.67: 2 residues within 4Å: Chain F: N.615, M.620 No protein-ligand interaction detected (PLIP) NAG-NAG.68: 1 residues within 4Å: Chain F: N.624 No protein-ligand interaction detected (PLIP) NAG-NAG.69: 2 residues within 4Å: Chain F: R.632, N.636 No protein-ligand interaction detected (PLIP)

1 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.9: 2 residues within 4Å: Chain B: N.183, N.185 No protein-ligand interaction detected (PLIP)

1 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.13: 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.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.208

1 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.14: 3 residues within 4Å: Chain B: N.273, T.275, D.276 No protein-ligand interaction detected (PLIP)

4 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.17: 6 residues within 4Å: Chain B: N.292, H.326, N.328, T.410, T.412 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 2 residues within 4Å: Chain D: N.130, T.186 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 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.48: 5 residues within 4Å: Chain E: N.130, T.132, D.184, T.186 Ligands: NAG-NAG-BMA.50 No protein-ligand interaction detected (PLIP)

3 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.18: 9 residues within 4Å: Chain B: R.331, N.335, T.390, W.391, N.394, G.395, T.396, W.397, T.400 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.391 Hydrogen bonds: B:W.397 NAG-NAG-BMA-MAN-MAN-MAN-MAN.41: 7 residues within 4Å: Chain D: R.331, T.332, N.335, W.391, N.394, N.398, T.400 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.391 NAG-NAG-BMA-MAN-MAN-MAN-MAN.60: 8 residues within 4Å: Chain E: T.332, N.335, N.392, N.394, G.395, T.396, T.400 Ligands: NAG-NAG.64 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.396

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.19: 3 residues within 4Å: Chain B: V.356, N.358, R.467 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.42: 4 residues within 4Å: Chain D: N.358, Q.359, N.388, H.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.49: 4 residues within 4Å: Chain E: N.153, Y.170, G.316, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.56: 2 residues within 4Å: Chain E: N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.59: 3 residues within 4Å: Chain E: H.326, N.328, T.410 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.323 NAG-NAG-BMA-MAN.62: 5 residues within 4Å: Chain E: Q.359, M.369, N.382, T.384 Ligands: NAG-NAG-BMA-MAN.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.63: 2 residues within 4Å: Chain E: N.388 Ligands: NAG-NAG-BMA-MAN.62 No protein-ligand interaction detected (PLIP)

3 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.24: 2 residues within 4Å: Chain C: N.610, S.612 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.45: 1 residues within 4Å: Chain D: N.398 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.66: 3 residues within 4Å: Chain F: N.610, S.612, Y.637 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.637

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.36: 13 residues within 4Å: Chain D: V.65, S.206, E.208, P.209, R.249, V.251, N.259, N.373, R.441, C.442, S.443, S.444 Ligands: NAG-NAG-BMA.46 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.443

2 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.40: 4 residues within 4Å: Chain D: N.292, N.328, T.410 Ligands: NAG-NAG-BMA.38 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.44: 3 residues within 4Å: Chain D: T.384, N.388 Ligands: NAG-NAG-BMA.43 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN.55: 6 residues within 4Å: Chain E: E.208, P.209, V.251, N.259, N.373 Ligands: NAG-NAG-BMA.65 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.70: 12 residues within 4Å: Chain B: I.109, W.112, D.113, L.116, V.252, S.371, F.378, I.421, M.423, W.424, K.429, M.431 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.112, B:L.116, B:V.252, B:F.378, B:F.378, B:I.421, B:W.424 Hydrogen bonds: B:D.113, B:W.424 pi-Stacking: B:W.424 83G.73: 13 residues within 4Å: Chain D: I.109, W.112, D.113, L.116, V.252, S.371, F.372, N.373, I.421, M.423, W.424, K.429, M.431 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.112, D:W.112, D:L.116, D:V.252, D:I.421, D:M.431 Hydrogen bonds: D:D.113, D:W.424 83G.75: 15 residues within 4Å: Chain E: I.109, W.112, D.113, L.116, V.252, T.254, S.371, N.373, F.378, I.421, N.422, M.423, W.424, K.429, M.431 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:W.112, E:L.116, E:F.378, E:I.421, E:W.424, E:M.431 Hydrogen bonds: E:D.113, E:W.424 pi-Stacking: E:W.424

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

NAG.71: 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.72: 2 residues within 4Å: Chain B: N.394, D.462 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.394 NAG.74: 1 residues within 4Å: Chain D: N.352 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.352 NAG.76: 2 residues within 4Å: Chain E: N.351, N.352 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.351

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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