SMTL ID : 7m8k.1

Cryo-EM structure of Brazil (P.1) SARS-CoV-2 spike glycoprotein variant in the prefusion state (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

11 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 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain C: T.716, N.717, F.718, N.919, L.922, Q.926, Q.1071, F.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.11: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: F.342, N.343, F.374 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.282, T.284 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: Y.28, N.61, R.634 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: K.1073, N.1074 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: C.1082, C.1126, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe (2021)

Release Date

2021-05-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein