SMTL ID : 7df4.1

SARS-CoV-2 S-ACE2 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

18 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 B: D.1127, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: A.706, N.1074 Chain D: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.709 Chain D: I.794, D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: Q.895 Chain C: S.704, V.705, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.717, T.719, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.925, C:Q.926 Hydrogen bonds: C:N.925 NAG-NAG.13: 4 residues within 4Å: Chain B: D.796 Chain C: Y.707, S.708, N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain D: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain D: N.717, L.922, N.925 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.925 Hydrogen bonds: D:N.925

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

NAG.19: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: D.614, N.616 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.343, S.373 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.234 Chain C: H.519 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.149 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.122, E.154, F.157 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: V.16, N.17, N.137 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.343, S.373 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: E.281, N.282 Chain D: K.558 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: T.108, N.234, T.236 Chain D: E.465 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.149, S.151 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: F.59, S.60, N.61 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: C.15, V.16, N.17, N.137, D.138 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: D.796 Chain D: N.709, N.710 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain D: N.616 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain D: F.338, G.339, F.342, N.343, V.367, S.371 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.280, N.282 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: K.462, E.465 Chain D: N.234, T.236 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain B: R.466 Chain D: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: N.149, S.151, M.153 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: N.122, E.154, F.157 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain D: C.15, N.17, N.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM. Sci Adv (2021)

Release Date

2020-12-16

Peptides

Angiotensin-converting enzyme 2: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Angiotensin-converting enzyme 2

Spike glycoprotein

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