SMTL ID : 8k5h.1

Structure of the SARS-CoV-2 BA.1 spike with UT28-RD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

8 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: 2 residues within 4Å: Chain A: N.705, Q.1059 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.789, S.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: R.445, K.450, E.453 Chain B: T.97, N.222 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.705, Q.1059 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.789, S.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: R.445, S.447, N.448, K.450 Chain C: T.97, N.222 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.705, Q.914 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.789, S.791, Q.792 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: Y.19, F.50, N.52 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.111, A.112, T.113, N.114 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.151 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.222 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.270 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.319, Q.568 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: F.330, N.331, V.355 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.604, T.606, Q.632 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.697 Chain B: Y.784 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1062 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.1086, T.1088, H.1089, F.1091 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.1122 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.19, N.52 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.111, A.112, T.113 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: Y.339, I.456 Chain B: N.150, N.151 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: K.546 Chain B: N.268, E.269, N.270 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.319, Q.568 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.331, L.359 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.591 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.604, T.606, Q.632 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.697 Chain C: Y.784 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: S.699, N.1062 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.1086, H.1089, F.1091 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1122 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.19, N.52 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.151 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.268, E.269, N.270 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.319, Q.568 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.591 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.604, T.606 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: Y.784 Chain C: S.696, N.697 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.1062 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.1086, T.1088, H.1089, F.1091 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1122 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozawa, T. et al., Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1. Structure (2024)

Release Date

2023-12-27

Peptides

Spike glycoprotein: ABC
UT28K-RD Fab heavy chain: D
UT28K-RD Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
H

E
L

Spike glycoprotein

UT28K-RD Fab heavy chain

UT28K-RD Fab light chain

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