SMTL ID : 7cn4.1

Cryo-EM structure of bat RaTG13 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 3 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.351 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.234, T.236 Chain B: R.457, A.459, N.460, K.462, E.465 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.458 NAG-NAG.4: 7 residues within 4Å: Chain B: N.234, T.236 Chain C: R.457, A.459, N.460, K.462, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.458 NAG-NAG.5: 7 residues within 4Å: Chain A: R.457, A.459, N.460, K.462, E.465 Chain C: N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458 NAG-NAG.6: 3 residues within 4Å: Chain B: N.164, N.165 Chain C: Y.351 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, S.155 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: Y.351 Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, S.155 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.370 Chain B: Y.493 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.29, N.30, D.215 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.370 Chain C: Y.493 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.713 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: T.29, N.30, D.215 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: Y.493 Chain C: N.370 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: T.29, N.30, D.215 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution. Nat Commun (2021)

Release Date

2021-03-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein