SMTL ID : 6xr8.1

Distinct conformational states of SARS-CoV-2 spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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.1: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 7 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG-MAN.7: 7 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, E.465 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.236 NAG-NAG-MAN.8: 1 residues within 4Å: Chain A: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 5 residues within 4Å: Chain A: N.616, T.618, Q.644, T.645 Chain B: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 5 residues within 4Å: Chain B: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG-MAN.19: 9 residues within 4Å: Chain A: R.457, S.459, N.460, L.461, K.462, E.465 Chain B: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.236 NAG-NAG-MAN.20: 1 residues within 4Å: Chain B: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 5 residues within 4Å: Chain B: N.616, T.618, Q.644, T.645 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.23: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG-MAN.31: 10 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, L.461, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.236 NAG-NAG-MAN.32: 1 residues within 4Å: Chain C: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 5 residues within 4Å: Chain A: I.834 Chain C: N.616, T.618, Q.644, T.645 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.34: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.35: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

9 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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.165 Chain C: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain A: Y.351, I.468 Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain B: Y.351, A.352 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP)

3 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.3: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP)

3 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.12: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.24: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.36: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.37: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: G.339, N.343, L.368, N.370, S.371 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: K.147, N.149 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: K.147, N.149, M.153 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: K.147, N.149 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1158 Ligand excluded by 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
A

B
B

C
C

Spike glycoprotein

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