SMTL ID : 7v79.1

Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), one RBD-up conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

33 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.581 NAG-NAG.5: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.11: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: S.112, E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: N.717, L.922 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.19: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain B: N.20, G.261 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain A: D.796 Chain C: S.708, N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.706 NAG-NAG.33: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

1 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.2: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP)

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

NAG.35: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: V.120, N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: Y.655, N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.20, T.22, W.258 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: K.187, N.188, H.207 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: Y.655, N.657 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: K.187, N.188 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.49: 6 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.331, I.332 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: Y.655, N.657 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.20, W.258 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: L.176, N.188, H.207, P.209 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), one RBD-up conformation 2. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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