SMTL ID : 6xra.1

Distinct conformational states of SARS-CoV-2 spike protein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: S.711, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: A.1190, N.1194 Chain C: Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: S.711, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: Q.935 Chain B: A.1190, N.1194 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: S.711, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: Q.935 Chain C: A.1190, N.1194 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.2: 4 residues within 4Å: Chain A: N.1098, H.1101, F.1103 Ligands: MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.3: 4 residues within 4Å: Chain A: N.1134, T.1136, D.1139 Chain C: I.726 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.7: 4 residues within 4Å: Chain B: N.1098, H.1101, F.1103 Ligands: MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.8: 4 residues within 4Å: Chain A: I.726 Chain B: N.1134, T.1136, D.1139 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.12: 4 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligands: MAN.26 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.13: 4 residues within 4Å: Chain B: I.726 Chain C: N.1134, T.1136, D.1139 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.4: 1 residues within 4Å: Chain A: N.1158 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 1 residues within 4Å: Chain B: N.1158 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 1 residues within 4Å: Chain C: N.1158 No protein-ligand interaction detected (PLIP)

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.16: 4 residues within 4Å: Chain A: Y.707, N.709, T.1076, S.1097 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.1076, A:S.1097 NAG.17: 1 residues within 4Å: Chain A: N.717 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.717 NAG.19: 1 residues within 4Å: Chain A: N.1173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1173 NAG.20: 4 residues within 4Å: Chain B: Y.707, N.709, T.1076, S.1097 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.1076, B:S.1097 NAG.21: 1 residues within 4Å: Chain B: N.717 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.717 NAG.23: 1 residues within 4Å: Chain B: N.1173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1173 NAG.24: 4 residues within 4Å: Chain C: Y.707, N.709, T.1076, S.1097 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.1076, C:S.1097 NAG.25: 1 residues within 4Å: Chain C: N.717 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.717 NAG.27: 1 residues within 4Å: Chain C: N.1173 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1173

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.18: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.2 No protein-ligand interaction detected (PLIP) MAN.22: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.7 No protein-ligand interaction detected (PLIP) MAN.26: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Y. et al., Distinct conformational states of SARS-CoV-2 spike protein. Science (2020)

Release Date

2020-07-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein

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