SMTL ID : 8z3w.1

Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

21 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.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 NAG-NAG.6: 6 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: K.147, N.148, N.149, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.717, L.922 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.20: 1 residues within 4Å: Chain C: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP)

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

NAG.22: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: H.146, N.149, M.153 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: Q.115, E.132, N.165, T.167 Chain C: R.357 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.122, T.124 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain A: R.457, L.461, K.462, E.465 Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, F.157 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: Y.144, K.147, N.149, M.153 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: K.462, E.465 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.616, Q.644 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 one ACE2 receptor binding (RB1) in prefusion conformation. To Be Published

Release Date

2025-02-05

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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