SMTL ID : 7ox4.1

Mouse interleukin-9 in complex with Fab 35D8.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.35, E.100, H.102 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.35, A:E.100, A:H.102, H2O.3 ZN.2: 2 residues within 4Å: Chain A: D.105, H.107 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.105, A:D.105, A:H.107, H2O.6 ZN.3: 1 residues within 4Å: Chain A: H.107 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.107 ZN.4: 2 residues within 4Å: Chain A: H.174 Chain B: D.140 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.174, B:D.140, B:D.140, H2O.6, H2O.10 ZN.6: 2 residues within 4Å: Chain B: D.84, H.104 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, B:D.84, B:H.104, H2O.10, H2O.10 ZN.7: 2 residues within 4Å: Chain B: H.199 Ligands: ACT.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.199, H2O.11, H2O.11 ZN.8: 2 residues within 4Å: Chain B: S.2, D.96 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.96, B:D.96, H2O.7, H2O.7, H2O.7 ZN.9: 1 residues within 4Å: Chain B: H.97 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.97, H2O.7, H2O.7 ZN.10: 3 residues within 4Å: Chain B: D.153, H.190, R.191 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.153, B:H.190, H2O.11 ZN.11: 1 residues within 4Å: Chain B: H.190 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.190, H2O.11, H2O.11 ZN.13: 1 residues within 4Å: Chain C: E.96 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 1 residues within 4Å: Chain A: D.218 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.216 ACT.12: 6 residues within 4Å: Chain B: A.114, P.115, H.199, S.202, V.204 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.204 Salt bridges: B:H.199 ACT.14: 6 residues within 4Å: Chain C: S.44, V.45, P.46, P.53, C.54, C.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.44, C:C.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Vos, T. et al., Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9). Biorxiv (2022)

Release Date

2022-12-28

Peptides

Heavy chain (Fab 35D8): A
Light chain (Fab 35D8): B
Interleukin-9: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Heavy chain (Fab 35D8)

Light chain (Fab 35D8)

Interleukin-9