SMTL ID : 7s3f.1

Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with its inhibitor 1-amino-oxy-3-aminopropane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 17 residues within 4Å: Chain A: A.67, K.69, D.88, A.111, R.154, L.166, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Chain B: C.360 Ligands: XAP.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.237, A:G.276, A:R.277, A:Y.389, A:Y.389 Water bridges: A:F.238, A:Y.278 Salt bridges: A:H.197 pi-Cation interactions: A:K.69, A:H.197 PLP.3: 15 residues within 4Å: Chain A: C.360 Chain B: A.67, K.69, D.88, R.154, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Ligands: XAP.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.237, B:G.276, B:R.277, B:Y.389, B:Y.389 Salt bridges: B:H.197, B:R.277 pi-Stacking: B:H.197

2 x XAP: 3-AMINOOXY-1-AMINOPROPANE(Non-covalent)

XAP.2: 8 residues within 4Å: Chain A: L.166, Y.331, D.332, Y.389 Chain B: Y.323, C.360, D.361 Ligands: PLP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.332 XAP.4: 8 residues within 4Å: Chain A: Y.323, D.361 Chain B: K.69, H.197, Y.331, D.332, Y.389 Ligands: PLP.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, X.E. et al., Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane. Biochem.J. (2021)

Release Date

2021-12-15

Peptides

Ornithine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ornithine decarboxylase

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