SMTL ID : 7kj3.1

SARS-CoV-2 Spike Glycoprotein with two ACE2 Bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

20 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.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.788, S.790, Q.791, F.804 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.804 NAG-NAG.5: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.704, N.906, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: I.1119, V.1120, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain D: N.43, T.45, N.328, Q.330 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain D: K.16, N.80 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain D: N.93 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain D: F.275, N.422 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain D: K.303, N.536 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: N.43, N.48, N.328, Q.330 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain E: N.80 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: Q.71, M.72, Q.91, N.93 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: F.275, N.422, W.584 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain E: K.303, N.536 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: N.109, A.110, T.111, N.112, V.114, K.116 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: T.95, N.221, T.223 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.269 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.318, Q.567, T.568 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.330, V.354, L.355 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: T.294, N.590 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.696, G.1118 Chain B: D.783 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.151, N.152 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: H.642, V.643, N.644 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.696 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.704, N.906, L.909, Q.1058 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: A.693, N.1061 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: R.344 Chain B: N.152 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.48 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.109, T.111, K.116 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.221, T.223 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.330 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.109, T.111, N.112, V.114 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: G.219, N.221 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.267, N.269 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.318, Q.567, T.568 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: G.326, N.330, L.355 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain A: D.783 Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: E.119, N.152 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain D: K.299, N.312 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain E: K.299, N.312 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
Angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Angiotensin-converting enzyme 2

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