SMTL ID : 7sc5.1

Cytoplasmic tail deleted HIV Env trimer in nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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: 9 residues within 4Å: Chain A: E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.181, A:G.348 NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: G.323, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 9 residues within 4Å: Chain C: E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.181, C:G.348 NAG-NAG-BMA.6: 2 residues within 4Å: Chain C: G.323, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 9 residues within 4Å: Chain E: E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.181, E:G.348 NAG-NAG-BMA.9: 2 residues within 4Å: Chain E: G.323, N.324 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: N.204, T.206, G.207, P.208, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.204, T.206, G.207, P.208, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain E: N.204, T.206, G.207, P.208, H.321 No protein-ligand interaction detected (PLIP)

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

NAG.10: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.271, V.410 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.232, P.261, S.415, N.416 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: S.357, G.358, L.359, F.360, N.361 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.355, S.357 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: L.56, E.57, N.58 Chain B: G.13, S.17 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: V.104, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain C: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.271, V.410 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: N.232, P.261, S.415, N.416 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: S.357, G.358, L.359, F.360, N.361 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.355, S.357 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: L.56, E.57, N.58 Chain D: G.13, S.17 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: V.104, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.114 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain E: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.271, V.410 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain E: N.232, P.261, S.415, N.416 Ligands: NAG-NAG-BMA.7 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain E: S.357, G.358, L.359, F.360, N.361 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.355, S.357 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain E: L.56, E.57, N.58 Chain F: G.13, S.17 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: V.104, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: N.107, S.109, E.110 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, S. et al., Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack. Nat Commun (2022)

Release Date

2022-11-09

Peptides

Envelope glycoprotein gp120: ACE
Transmembrane protein gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Envelope glycoprotein gp120

Transmembrane protein gp41