SMTL ID : 7tf5.1

Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

36 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: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 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: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: S.704, A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: S.704, A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain D: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain D: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.922 NAG-NAG.21: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain E: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.922 NAG-NAG.27: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain E: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain E: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain F: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain F: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.922 NAG-NAG.33: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 1 residues within 4Å: Chain F: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.37: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: F.338, F.342, N.343 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: F.338, F.342, N.343 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: N.122, T.124, V.127, F.157 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain B: R.466, I.468 Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain B: K.462 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain D: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain D: E.132, N.164, N.165 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain D: T.108, N.234, T.236 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain D: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain D: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain D: N.709, I.1130, G.1131 Chain E: D.796 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain E: Y.28, N.61 Ligand excluded by PLIP NAG.70: 6 residues within 4Å: Chain E: N.122, A.123, T.124, N.125, V.127, F.157 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain E: E.132, N.164, N.165 Ligand excluded by PLIP NAG.72: 4 residues within 4Å: Chain D: E.465 Chain E: T.108, N.234, T.236 Ligand excluded by PLIP NAG.73: 3 residues within 4Å: Chain D: K.558 Chain E: N.280, N.282 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain E: N.331, Q.580 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain E: F.338, F.342, N.343 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.77: 2 residues within 4Å: Chain F: Y.28, N.61 Ligand excluded by PLIP NAG.78: 4 residues within 4Å: Chain F: N.122, T.124, V.127, F.157 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain F: E.132, N.164, N.165 Ligand excluded by PLIP NAG.80: 3 residues within 4Å: Chain F: T.108, N.234, T.236 Ligand excluded by PLIP NAG.81: 3 residues within 4Å: Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain F: N.331, Q.580 Ligand excluded by PLIP NAG.83: 4 residues within 4Å: Chain F: F.342, N.343, V.367, L.368 Ligand excluded by PLIP NAG.84: 4 residues within 4Å: Chain D: D.796 Chain F: N.709, I.1130, G.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Nat Commun (2022)

Release Date

2022-03-30

Peptides

Spike glycoprotein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

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