SMTL ID : 7soe.1

SARS-CoV-2 S B.1.617.1 kappa variant + S2X303 Global Refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 6 residues within 4Å: Chain A: N.122, A.123, N.125 Chain C: N.30, T.31, G.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.32 NAG-NAG.2: 6 residues within 4Å: Chain D: N.122, A.123, N.125 Chain F: N.30, T.31, G.32 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.32 NAG-NAG.3: 6 residues within 4Å: Chain G: N.122, A.123, N.125 Chain I: N.30, T.31, G.32 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.32

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

NAG.4: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.717, Q.926 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: K.147, N.148, N.149 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.17 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.801, S.803 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.717, Q.926 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: F.59, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.280, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain D: N.234 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: K.147, N.148, N.149 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.17 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: G.339, F.342, N.343 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: H.655, N.657 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.616, T.618 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.801, S.803 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: N.717, Q.926 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: F.59, N.61 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain G: N.280, N.282 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.164, N.165 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain G: N.234 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: K.147, N.148, N.149 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain G: N.17 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain G: G.339, F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science (2021)

Release Date

2021-11-17

Peptides

Spike glycoprotein: ADG
S2X303 Fab light chain: BEH
S2X303 Fab heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

G
F

B
L

E
D

H
G

C
B

F
E

I
H

Spike glycoprotein

S2X303 Fab light chain

S2X303 Fab heavy chain

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