SMTL ID : 8hc3.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-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: 2 residues within 4Å: Chain A: I.1112, 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 C: N.697, L.902, Q.906, Q.1051 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1114 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.107, T.109, N.110, V.112 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: E.117, N.146, N.147 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.218 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.264, E.265, N.266 Chain B: K.542 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: F.326, N.327, N.354, L.355 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: 3 residues within 4Å: Chain A: N.689, G.1111 Chain C: Y.776 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: S.47, N.48 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: N.107, T.109, N.110, V.111, V.112, F.139 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.146, N.147 Ligand excluded by PLIP NAG.26: 8 residues within 4Å: Chain B: T.93, N.218, T.220 Chain C: R.441, S.443, N.444, L.445, K.446 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.266 Chain C: K.542 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: F.313, N.315, Q.564 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: F.326, N.327, N.354 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.600, T.602, E.603, T.629 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.689, G.1111 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Q.875 Chain B: A.686, E.1052, N.1054 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.107, T.109, V.112 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: Q.100, E.117, N.147 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: H.503 Chain C: N.218 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: K.542 Chain C: E.265, N.266 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: R.312, N.315, Q.564 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: D.323, N.327, W.420 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.600, T.602, E.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.689, N.690 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: Q.875 Chain C: A.686, E.1052, 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: ABC
Light chain of YB9-258: DF
Heavy chain of YB9-258: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

F
E

E
H

G
D

Spike glycoprotein

Light chain of YB9-258

Heavy chain of YB9-258

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