SMTL ID : 5x58.1

Prefusion structure of SARS-CoV spike glycoprotein, conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.678 Chain B: L.763 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.686, Q.891 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: Y.765, N.770 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.1043 Chain B: Q.864 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: S.340, V.341, N.344 Ligand excluded by PLIP NAG.6: 6 residues within 4Å: Chain A: F.312, G.313, F.316, N.317, V.341, F.347 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.305, K.553 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: E.255, N.256 Chain C: R.531 Ligand excluded by PLIP NAG.9: 7 residues within 4Å: Chain A: T.93, N.214, T.216 Chain C: R.431, K.434, R.436, E.439 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: F.144, N.145 Chain C: Y.325, A.326, I.442 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Q.19, N.52, R.607 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.96, E.118, N.142, F.144 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.589, Q.617 Chain B: I.819 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.589, T.591, Q.617 Chain C: I.819 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.678 Chain C: L.763 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.686, N.888, Q.891 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: Y.765, N.770 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: E.1041, N.1043 Chain C: Q.864 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: S.340, V.341, N.344 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: F.312, G.313, F.316, N.317, V.341, F.347 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.305, K.553 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: R.531 Chain B: E.255, N.256 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain A: R.431, K.434, R.436, E.439 Chain B: T.93, N.214, T.216 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: Y.325, A.326, I.442 Chain B: F.144, N.145 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Q.19, N.52, R.607 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.96, E.118, N.142, F.144 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: I.819 Chain C: N.589, T.591, Q.617 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: L.763 Chain C: N.678 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.686, Q.891 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.765, N.770 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: Q.864 Chain C: E.1041, N.1043 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: S.340, V.341, N.344 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain C: F.312, G.313, F.316, N.317, V.341, F.347 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.305, K.553 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: R.531 Chain C: E.255, N.256 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain B: R.431, K.434, R.436, E.439 Chain C: T.93, N.214, T.216 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: Y.325, A.326, I.442 Chain C: N.145 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: Q.19, N.52, R.607 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.96, E.118, N.142, F.144 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, Y. et al., Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun (2017)

Release Date

2017-05-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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