SMTL ID : 7v7a.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

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

NAG-NAG.2: 2 residues within 4Å: Chain A: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.709, G.1131 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.20 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: E.281, 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: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain A: D.796 Chain B: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.706 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: 3 residues within 4Å: Chain C: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: D.796 Chain C: S.708, N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain B: Q.895 Chain C: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.33: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: K.187, N.188, P.209 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain B: V.120, N.122, T.124, V.127, L.141, F.157 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: Q.115, N.165, C.166, T.167 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.20 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: L.176, K.187, N.188, H.207 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: V.120, N.122, T.124, V.127, F.157 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.20, T.22 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain C: K.187, N.188, H.207, T.208, 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), two RBD-up conformation. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Spike glycoprotein

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