SMTL ID : 7sob.1

SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.331, P.579 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.717, Q.926, H.1071 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.61 Chain C: S.75 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.122, A.123 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: C.15, N.17 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain F: N.331, P.579 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain F: H.655, N.657 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain F: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain F: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain F: N.1134 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: N.616, T.618 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain F: N.709, G.1131 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain F: N.282 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain F: N.801, S.803 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain F: N.717, Q.926, H.1071 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain F: N.61 Chain H: S.75 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: N.122, A.123 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain F: N.234 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: C.15, N.17 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain F: N.164, N.165 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: G.339, F.342, N.343 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain K: N.331, P.579 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain K: N.603 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain K: H.655, N.657 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain K: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain K: N.1134 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain K: N.616, T.618 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain K: N.709, G.1131 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain K: N.282 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain K: N.801, S.803 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain K: N.717, Q.926, H.1071 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: N.61 Chain M: S.75 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain K: N.122, A.123 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain K: N.234 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain K: C.15, N.17 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain K: N.164, N.165 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain K: 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: AFK
S2L20 Fab light chain: BGL
S2L20 Fab heavy chain: CHM
S309 Fab heavy chain: DIN
S309 Fab light chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
D

K
K

B
B

G
E

L
L

C
C

H
F

M
M

D
G

I
H

N
N

E
I

J
J

O
O

Spike glycoprotein

S2L20 Fab light chain

S2L20 Fab heavy chain

S309 Fab heavy chain

S309 Fab light chain

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