SMTL ID : 8r1c.1

SD1-2 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: 3 residues within 4Å: Chain A: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.706 Chain H: Y.793 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain H: I.831, Q.833 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1071, F.1072, T.1073, S.1094 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.231 Chain I: E.462 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain H: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain H: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain H: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain H: N.1131 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain H: N.706 Chain I: Y.793 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain H: N.613, T.615, Q.641 Chain I: I.831, Q.833 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain H: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain H: N.277, E.278, N.279 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain H: N.1071, F.1072, T.1073, S.1094 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.462 Chain H: N.231 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain I: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain I: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain I: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain I: N.1131 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.793 Chain I: N.706 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: I.831, Q.833 Chain I: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain I: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain I: N.277, E.278, N.279 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain I: N.1071, F.1072, T.1073, S.1094 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain H: E.462 Chain I: N.231 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

Spike glycoprotein,Fibritin: AHI
SD1-2 fab heavy chain: BDF
SD1-2 fab light chain: CEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
B

I
C

B
H

D
D

F
F

C
L

E
E

G
G

Spike glycoprotein,Fibritin

SD1-2 fab heavy chain

SD1-2 fab light chain

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