SMTL ID : 4jzj.1

Crystal Structure of Receptor-Fab Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUL- FUL: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUL-FUL.1: 15 residues within 4Å: Chain A: A.37, N.61, T.63, S.72, W.74, L.76 Chain E: N.55, G.56, A.57, T.58, F.59, Y.60, Q.62, K.65 Chain F: Y.100 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:T.58, E:Y.60, A:S.72, E:T.58, E:T.58 Hydrophobic interactions: E:A.57, E:F.59

1 x NAG- NAG- BMA- FUL- FUL: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUL-FUL.2: 11 residues within 4Å: Chain B: A.37, N.61, T.63, S.72, W.74 Chain C: G.56, A.57, T.58, F.59, Y.60, K.65 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.63, C:K.65, C:T.58

1 x NAG- FUC- FUL: alpha-L-fucopyranose-(1-3)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-FUL.3: 4 residues within 4Å: Chain B: E.89, N.90, A.106 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.106 Hydrogen bonds: B:E.89, B:E.89, B:N.90

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

NAG.4: 3 residues within 4Å: Chain A: N.27, V.28, T.29 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Ligands: NAG-FUC-FUL.3, NAG-FUC-FUL.3 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain B: L.56, R.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.165, B:R.165 GOL.7: 8 residues within 4Å: Chain E: P.174, V.176, S.184, L.185, S.186 Chain F: S.168, S.182, T.184 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:V.176, E:S.186, F:S.168, F:S.182 Water bridges: F:T.184, F:T.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broughton, S.E. et al., Dual mechanism of interleukin-3 receptor blockade by an anti-cancer antibody. Cell Rep (2014)

Release Date

2014-04-09

Peptides

Interleukin-3 receptor subunit alpha: AB
Fab Heavy Chain: CE
Fab Light Chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

E
H

D
B

F
L

Interleukin-3 receptor subunit alpha

Fab Heavy Chain

Fab Light Chain