SMTL ID : 8h3n.1

Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 7 residues within 4Å: Chain A: T.106, N.231, T.233 Chain E: R.454, S.456, K.459, E.462 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain A: A.700, E.1066, K.1067, N.1068 Chain D: Q.889 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.1128 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.1092, T.1094, H.1095, F.1097 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: N.613, T.615, E.616 Chain D: I.828, Q.830 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.703 Chain D: I.788, Y.790 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.795, S.797, Q.798 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, V.364 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.711, L.916, Q.920, Q.1065 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain D: N.328, Q.577 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain D: A.700, E.1066, K.1067, N.1068 Chain E: Q.889 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain D: I.1126, N.1128 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain D: N.1092, T.1094, H.1095, F.1097, P.1106 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.613, E.616 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.703 Chain E: Y.790 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain D: N.795, S.797, Q.798 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: E.278, N.279 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: F.59, N.61, P.628 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.711, Q.920, Q.1065 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain E: T.106, T.233 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: A.700, E.1066, N.1068 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain E: N.1128 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: N.1092, H.1095, F.1097 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain E: N.613, T.615 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.790 Chain E: N.703 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: N.795, S.797 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain E: N.711, L.916, Q.920, Q.1065 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishimaru, H. et al., Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants. J.Virol. (2023)

Release Date

2023-05-10

Peptides

Spike glycoprotein: ADE
MO1 heavy-chain: BF
MO1 light chain: CG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

B
D

F
H

C
E

G
I

Spike glycoprotein

MO1 heavy-chain

MO1 light chain

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