SMTL ID : 7qti.1

SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-3-mer

Ligands

14 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: 1 residues within 4Å: Chain I: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain I: D.336, F.339, N.340, V.364, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain I: S.705, N.706 Chain K: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain I: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.919 NAG-NAG.5: 2 residues within 4Å: Chain I: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain I: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain J: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain J: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain J: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain J: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:L.919 NAG-NAG.11: 3 residues within 4Å: Chain I: K.555 Chain K: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain K: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain K: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain K: N.1131 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.13: 3 residues within 4Å: Chain K: D.336, F.339, N.340 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.16: 4 residues within 4Å: Chain K: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:L.919 NAG-NAG-BMA.17: 2 residues within 4Å: Chain K: N.798, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.18: 2 residues within 4Å: Chain I: N.328, Q.577 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain I: N.613, E.616 Chain K: G.835 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain I: Y.652, N.654 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain I: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain I: I.1129, N.1131 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain I: N.120, A.121, T.122, N.123, V.125 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain I: T.19, C.134, N.135 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain I: S.110, K.111, N.159, N.160 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain J: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain J: N.706 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain J: Y.28, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain J: D.336, N.340, L.368 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain J: N.600 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain I: Y.834, D.836 Chain J: N.613, T.615 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain J: N.654 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain J: E.1069, N.1071 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain J: N.798, Q.801 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain J: N.120, A.121, N.123 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain J: E.130, N.159, N.160 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain J: N.231 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain J: G.835, D.836 Chain K: N.613, T.615 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain K: N.654 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain K: N.1071 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain J: Y.793 Chain K: N.706 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain K: N.120, A.121, T.122, N.123, V.125, E.149 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain K: N.159, N.160 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, C. et al., Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys. Nat Microbiol (2022)

Release Date

2022-08-03

Peptides

P2G3 Heavy Chain: ACG
P2G3 Light Chain: BDH
P5C3 Light Chain: E
P5C3 Heavy Chain: F
Spike glycoprotein,Envelope glycoprotein: IJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
B

G
I

B
H

D
C

H
J

E
E

F
F

I
D

J
K

K
A

P2G3 Heavy Chain

P2G3 Light Chain

P5C3 Light Chain

P5C3 Heavy Chain

Spike glycoprotein,Envelope glycoprotein

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