SMTL ID : 7s3g.1

Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 16 residues within 4Å: Chain A: A.67, K.69, D.88, A.111, R.154, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Chain B: C.360 Ligands: CIT.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.67, A:K.69 Hydrogen bonds: A:G.237, A:G.276, A:R.277, A:Y.389, A:Y.389 Water bridges: A:F.238, B:C.360 Salt bridges: A:H.197, A:R.277 pi-Cation interactions: A:H.197 PLP.3: 16 residues within 4Å: Chain A: C.360 Chain B: A.67, K.69, D.88, A.111, R.154, H.197, S.200, G.236, G.237, E.274, P.275, G.276, R.277, Y.389 Ligands: CIT.4 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.67, B:K.69 Hydrogen bonds: B:K.69, B:G.237, B:G.276, B:R.277, B:Y.389, B:Y.389 Water bridges: B:F.238, A:C.360 Salt bridges: B:H.197, B:R.277 pi-Cation interactions: B:H.197

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 12 residues within 4Å: Chain A: K.69, R.154, H.197, G.199, S.200, R.277, D.332, Y.389 Chain B: C.360, D.361, G.362 Ligands: PLP.1 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:D.361, B:G.362, A:R.154, A:S.200, A:S.200, A:Y.389 Water bridges: B:Y.323, B:Y.323, B:C.360, A:G.201, A:R.277, A:R.277 Salt bridges: A:H.197, A:H.197, A:R.277 CIT.4: 11 residues within 4Å: Chain A: C.360, D.361, G.362 Chain B: K.69, H.197, G.199, S.200, R.277, D.332, Y.389 Ligands: PLP.3 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.361, A:G.362, B:R.154, B:S.200, B:S.200 Water bridges: A:Y.323, A:Y.323, A:C.360, A:D.361, A:D.361, A:D.361, A:L.363, B:G.201, B:R.277, B:R.277 Salt bridges: B:H.197, B:H.197, B:R.277

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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