SMTL ID : 7r1b.1

Mink Variant SARS-CoV-2 Spike with 1 Erect RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

8 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: N.746, L.951 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1127, T.1129, H.1130, F.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 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.4: 4 residues within 4Å: Chain B: N.1127, T.1129, H.1130, F.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.360, Q.609 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.1127, T.1129, H.1130, F.1132 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.8: 3 residues within 4Å: Chain C: N.830, S.832, Q.833 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.309, E.310, N.311 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.360, Q.609, L.611 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.645 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.686 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.738, G.1160 Chain B: D.825 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.830, S.832, Q.833 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.372 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.735, E.1101, N.1103 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1163 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: T.137, N.263, T.265 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.309, E.310, N.311 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.632 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.645, T.647 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.830, S.832, Q.833 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: A.735, E.1101, K.1102, N.1103 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.738, G.1160 Chain C: D.825 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1163 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1163 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: Q.924 Chain C: A.735, E.1101, K.1102, N.1103 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.309, E.310, N.311 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.632 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: H.684, V.685, N.686 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.738, N.739, G.1160 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.360, Q.609 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.645, Q.673 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: G.368, F.371, N.372, S.400 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

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