SMTL ID : 7df3.1

SARS-CoV-2 S trimer, S-closed

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

24 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: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG.3: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925, A:Q.926 Hydrogen bonds: A:N.925 NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 10 residues within 4Å: Chain A: T.108, N.234, T.236, R.237 Chain C: R.457, K.458, S.459, N.460, L.461, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.165 Chain C: A.352 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.8: 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.9: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG.11: 5 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925, B:Q.926 Hydrogen bonds: B:N.925 NAG-NAG.12: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 10 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, L.461, E.465 Chain B: T.108, N.234, T.236, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain A: A.352 Chain B: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.16: 3 residues within 4Å: Chain B: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 NAG-NAG.17: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101 NAG-NAG.19: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925, C:Q.926 Hydrogen bonds: C:N.925 NAG-NAG.20: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 10 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, L.461, E.465 Chain C: T.108, N.234, T.236, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain B: A.352 Chain C: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.24: 3 residues within 4Å: Chain C: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.137

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

NAG.25: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.709, N.710 Chain B: D.796 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: V.615, N.616, Q.644 Chain B: I.834, Q.836 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.343, V.367, S.371 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: Y.144, N.149, M.153 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.709, N.710 Chain C: D.796 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: V.615, N.616, Q.644 Chain C: I.834, Q.836 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.343, V.367, S.371 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: Y.144, N.149, M.153 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain A: I.834, Q.836 Chain C: V.615, N.616, Q.644 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.343, V.367, S.371 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: Y.144, N.149, M.153 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: Y.28, N.61 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

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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