SMTL ID : 8xym.1

Cryo-EM structure of CX1 spike protein (6P)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

5 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.122, T.124, N.125, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: T.108, N.234 Chain C: R.457, S.459, N.460 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.370 Chain C: F.456, Y.489, Q.493 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.705, G.1127 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.30 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1070 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.30, D.215 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: H.146, N.149, S.151, M.153 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.351 Chain B: N.165 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain A: R.457, S.459, N.460, E.465 Chain B: T.108, N.234 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: F.456, Y.489, Q.493 Chain B: N.370 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.705, G.1127 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.1094, H.1097 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: T.29, N.30, F.59 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: R.457, S.459, N.460, K.462 Chain C: N.234, T.236 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: Y.489, Q.493 Chain C: N.370 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.705, G.1127 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.713, Q.1067 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.797, S.799 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: E.1068, N.1070 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z.P. et al., Structural resemblances of bat-origin coronaviruses CX1 and BANAL-20-52 spikes provide further evidence on bat origination of SARS-CoV-2. To Be Published

Release Date

2025-01-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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