SMTL ID : 7sbr.1

One RBD-up 2 of pre-fusion SARS-CoV-2 Kappa variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

homo-trimer

Ligands

19 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: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.5: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 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: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.717, L.922, N.925, Q.1071 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.922 Hydrogen bonds: B:N.925 NAG-NAG.17: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.122, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.24: 5 residues within 4Å: Chain B: K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain A: Q.836 Chain C: N.616, T.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.836 NAG-NAG.27: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.28: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.6: 2 residues within 4Å: Chain A: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.29: 2 residues within 4Å: Chain C: E.1072, N.1074 No protein-ligand interaction detected (PLIP)

11 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.7: 4 residues within 4Å: Chain A: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 3 residues within 4Å: Chain A: S.112, E.132, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 3 residues within 4Å: Chain A: G.339, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 4 residues within 4Å: Chain B: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 3 residues within 4Å: Chain B: F.338, G.339, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 4 residues within 4Å: Chain C: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.31: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 5 residues within 4Å: Chain B: A.352, I.468 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 5 residues within 4Å: Chain B: N.487, Y.489 Chain C: F.342, N.343, F.374 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.487, B:Y.489

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

NAG.34: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: K.147, N.149 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.234, T.236 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: Y.1155, N.1158 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.149 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: K.147, N.149 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science (2021)

Release Date

2021-11-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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