SMTL ID : 7kj5.1

SARS-CoV-2 Spike Glycoprotein, prefusion with one RBD up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.221, T.223 Chain C: E.452 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.3: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.1085, T.1087, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.909 NAG-NAG.10: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: Y.15, T.16, N.17, N.48 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.109, N.112, V.114 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.267, N.269 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.318, P.566, Q.567 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: F.325, G.326, F.329, N.330, L.355 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.109, A.110, V.114, K.116 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.221, T.223 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: K.545 Chain B: N.267, E.268, N.269 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: F.325, G.326, F.329, N.330, V.354, L.355 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.704, N.906, L.909 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.1059, N.1061 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: S.99, E.119, N.151, N.152 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.109 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: G.219, N.221 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.267, N.269 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: F.325, G.326, N.330, L.355 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.119, N.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, T. et al., A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent. Nat.Struct.Mol.Biol. (2021)

Release Date

2020-11-11

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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