SMTL ID : 8z4x.1

Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.122, A.123, T.124, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: F.338, G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.709, G.1131 Chain D: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: H.146, N.149, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: G.339, N.343, S.371, S.373 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.137 NAG-NAG.19: 2 residues within 4Å: Chain E: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain E: N.1134 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain E: N.122, T.124, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.24: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: K.147, N.149 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain E: K.558 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.322 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: H.417, S.420, D.543, N.546 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: P.321, N.322 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain D: N.122, T.124, V.127, V.171 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: K.462, E.465 Chain D: N.234, T.236 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: N.616, Q.644 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain D: H.655, V.656, N.657 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: N.709, G.1131 Chain E: D.796 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain E: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: E.132, N.165 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.234 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: N.280, E.281, N.282 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain E: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: H.655, N.657 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation. To Be Published

Release Date

2025-02-05

Peptides

Spike glycoprotein: ADE
Angiotensin-converting enzyme 2: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
B

E
A

B
E

C
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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