SMTL ID : 7tm0.1

SARS-CoV-2 S B.1.1.529 Omicron variant + S309 + S2L20 Global Refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 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: 4 residues within 4Å: Chain B: Y.793, N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: D.336, F.339, N.340 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: C.15, N.17 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.231 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.120 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: Y.793, N.798, S.800, Q.801 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: D.336, F.339, N.340 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: C.15, N.17 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.120, T.122 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: Q.892 Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.328, I.329, Q.577 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: D.336, F.339, N.340 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.159, N.160 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: K.555 Chain C: N.277, N.279 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: C.15, N.17 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.120 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: Y.793, N.798, S.800 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: Q.892 Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.600, T.601 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science (2022)

Release Date

2022-02-02

Peptides

Spike glycoprotein: ABC
S2L20 Fab light chain: DFH
S2L20 Fab heavy chain: EGI
S309 Fab Heavy Chain: JLN
S309 Fab light chain: KMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

J
J

L
L

N
N

K
K

M
M

O
O

Spike glycoprotein

S2L20 Fab light chain

S2L20 Fab heavy chain

S309 Fab Heavy Chain

S309 Fab light chain

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