SMTL ID : 8c2r.1

SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.692, L.897, Q.901, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.679, V.680, A.681, E.1047, N.1049 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1073, T.1075, H.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.692, L.897, Q.901 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: S.679, V.680, A.681, N.1049 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1073, T.1075, H.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.692, L.897, Q.901 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: S.679, A.681, E.1047, N.1049 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.1073, T.1075, H.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: C.1057, N.1109 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: Y.3, N.5, N.36 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: T.99, N.100 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.139, N.140, C.141, T.142 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain A: N.171, G.174, I.208, N.209 Chain C: K.437, E.440 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.255, E.256, N.257 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.306, P.554, Q.555 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: D.314, N.318, V.342, L.346 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.684 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.3, N.36 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.97, T.99, N.100 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: E.107, N.139, N.140 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.209, T.211 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.255, N.257 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.306, Q.555 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: D.314, N.318, V.342, L.343, L.346, F.349 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.684 Chain C: Y.771 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.3, N.36 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.97, T.99, V.102 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: E.107, N.139, N.140 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: T.83, N.209, T.211 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.255, E.256, N.257 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: Y.771 Chain C: N.684 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheward, D.J. et al., Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med (2024)

Release Date

2024-05-22

Peptides

Spike glycoprotein: ABC
CAB-A17 antibody (LC): DF
CAB-A17 antibody (HC): EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

F
L

E
F

G
R

Spike glycoprotein

CAB-A17 antibody (LC)

CAB-A17 antibody (HC)