SMTL ID : 6zge.1

Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

30 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: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.153, T.155, N.156, V.158, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: E.163, N.195, N.196 Chain C: Y.382, A.383 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain A: T.139, N.265, T.267 Chain C: R.488, K.489, S.490, N.491, K.493, E.496 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.647, Q.675 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.748, L.953, Q.957, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.153, T.155, N.156, V.158, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain A: Y.382, A.383 Chain B: E.163, N.195, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 9 residues within 4Å: Chain A: R.488, K.489, S.490, N.491, K.493, E.496 Chain B: T.139, N.265, T.267 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.647, Q.675 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.748, L.953, Q.957, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: N.153, T.155, N.156, V.158, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain B: Y.382, A.383 Chain C: E.163, N.195, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 9 residues within 4Å: Chain B: R.488, K.489, S.490, N.491, K.493, E.496 Chain C: T.139, N.265, T.267 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.647, Q.675 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: N.748, L.953, Q.957, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1165 No protein-ligand interaction detected (PLIP)

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

NAG.31: 5 residues within 4Å: Chain A: H.177, N.179, N.180, S.182, M.184 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.311, E.312, N.313 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.374, S.402 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: N.740, I.1161, G.1162 Chain B: D.827 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: H.177, N.179, N.180, S.182, M.184 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.311, E.312, N.313 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.374, S.402 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.688 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: N.740, I.1161, G.1162 Chain C: D.827 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: H.177, N.179, N.180, S.182, M.184 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.311, E.312, N.313 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.374, S.402 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain A: D.827 Chain C: N.740, I.1161, G.1162 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: A.737, E.1103, N.1105 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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