SMTL ID : 7r18.1

Mink Variant SARS-CoV-2 Spike in Closed conformation

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain A: N.746, L.951, Q.955, Q.1100 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.951 NAG-NAG.3: 1 residues within 4Å: Chain A: N.1163 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.746, L.951, Q.955, Q.1100 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.951 NAG-NAG.6: 1 residues within 4Å: Chain B: N.1163 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.746, L.951, Q.955, Q.1100 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.951 NAG-NAG.9: 1 residues within 4Å: Chain C: N.1163 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.2: 6 residues within 4Å: Chain A: N.1127, T.1129, H.1130, F.1132, Y.1139, P.1141 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1141 NAG-NAG-FUC.5: 6 residues within 4Å: Chain B: N.1127, T.1129, H.1130, F.1132, Y.1139, P.1141 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.1141 NAG-NAG-FUC.8: 6 residues within 4Å: Chain C: N.1127, T.1129, H.1130, F.1132, Y.1139, P.1141 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.1141

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

NAG.10: 3 residues within 4Å: Chain A: N.360, Q.609, L.611 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: C.46, V.47, N.48, N.166 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: N.151, A.152, T.153, V.156, E.183 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.193, N.194 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: T.137, N.263 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: F.367, G.368, N.372, L.397 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.645, Q.673 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.686 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.738, G.1160 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.830, S.832, Q.833 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.1101, N.1103 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.309, E.310, N.311 Chain C: K.587 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.59, N.92 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.360, Q.609, L.611 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: C.46, V.47, N.48, N.166 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: N.151, A.152, T.153, V.156, E.183 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.193, N.194 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.137, N.263 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: F.367, G.368, N.372, L.397 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.645, Q.673 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.686 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.738, G.1160 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.830, S.832, Q.833 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.1101, N.1103 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: K.587 Chain B: N.309, E.310, N.311 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: Y.59, N.92 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.360, Q.609, L.611 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: C.46, V.47, N.48, N.166 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.151, A.152, T.153, V.156, E.183 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.193, N.194 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: T.137, N.263 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: F.367, G.368, N.372, L.397 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.645, Q.673 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.686 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.738, G.1160 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.830, S.832, Q.833 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.1101, N.1103 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: K.587 Chain C: N.309, E.310, N.311 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.59, N.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., Evolution of the SARS-CoV-2 spike protein in the human host. Nat Commun (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein