SMTL ID : 8hc2.1

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

12 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 A: N.697, L.902, Q.906, Q.1051 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.697, L.902, Q.906, Q.1051 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.697, L.902, Q.906, Q.1051 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain E: N.1114 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.48 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: N.107, T.109, N.110, V.111, V.112, F.139 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.146, N.147 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain A: N.218, T.220 Chain B: R.441, S.443, N.444, K.446 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.266 Chain B: K.542 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: R.312, F.313, N.315, T.317, Q.564 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: D.323, N.327 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.600, T.602, E.603, Q.628 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.689 Chain E: G.778 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: A.686, E.1052, N.1054 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.107, T.109, V.112 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.117, N.146, N.147 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.218, T.220 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.266 Chain E: K.542 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.315 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: D.323, N.327 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.600, E.603, Q.628 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.689, N.690 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: A.686, E.1052, N.1054 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.107, T.109, V.112 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: E.117, N.147 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain E: N.218 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: K.542 Chain E: N.266 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.315, I.316, T.317, V.346 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: D.323, N.327 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain E: N.600, T.602, E.603, Q.628 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.776 Chain E: N.689 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: A.686, N.1054 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants. Nat Commun (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: ABE
Light chain of YB9-258 Fab: C
Heavy chain of YB9-258 Fab: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

E
A

C
L

D
H

Spike glycoprotein

Light chain of YB9-258 Fab

Heavy chain of YB9-258 Fab

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