SMTL ID : 8r1d.1

SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain E: Y.25, N.58 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain E: N.277, E.278, N.279 Chain I: K.26, N.29 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain E: N.613, T.615, Q.641 Chain G: I.831, Q.833 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain E: N.654 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain E: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain E: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain E: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain E: N.1131 Ligand excluded by PLIP NAG.9: 8 residues within 4Å: Chain E: T.105, N.231, T.233 Chain F: R.454, S.456, N.457, K.459, E.462 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain E: N.706 Chain G: Y.793 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain F: Y.25, N.58 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain F: N.277, E.278, N.279 Chain H: K.26, N.29 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain E: I.831, Q.833 Chain F: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain F: Y.652, N.654 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain F: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain F: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain F: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain F: N.1131 Ligand excluded by PLIP NAG.19: 8 residues within 4Å: Chain F: T.105, N.231, T.233 Chain G: R.454, S.456, N.457, K.459, E.462 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain E: Y.793 Chain F: N.706 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain G: Y.25, N.58 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain D: K.26, N.29 Chain G: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain F: I.831, Q.833 Chain G: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain G: Y.652, N.654 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain G: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain G: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain G: N.1131 Ligand excluded by PLIP NAG.29: 8 residues within 4Å: Chain E: R.454, S.456, N.457, K.459, E.462 Chain G: T.105, N.231, T.233 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: Y.793 Chain G: N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, D. et al., The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun (2024)

Release Date

2024-03-13

Peptides

SD1-3 Fab Heavy Chain: ABC
SD1-3 Fab Light Chain: DHI
Spike glycoprotein,Fibritin: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
D

C
H

D
L

H
E

I
G

E
A

F
B

G
C

SD1-3 Fab Heavy Chain

SD1-3 Fab Light Chain

Spike glycoprotein,Fibritin

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