SMTL ID : 2oo0.1

A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: S.145, E.146, L.190 Chain B: K.304, I.305 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.146, A:L.190 Water bridges: A:D.144, A:E.146 Hydrogen bonds: B:I.305 ACT.2: 4 residues within 4Å: Chain A: K.304, I.305 Chain B: S.145, E.146 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.304 Hydrogen bonds: A:I.305, A:I.305, B:E.146 Water bridges: B:V.147, B:V.147 ACT.6: 6 residues within 4Å: Chain B: F.14, A.92, W.424, M.427, Q.428, Q.431 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.424 Hydrogen bonds: B:Q.428, B:Q.428, B:Q.431

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

PLP.3: 17 residues within 4Å: Chain A: A.77, K.79, D.98, A.121, R.164, L.176, H.207, S.210, G.246, G.247, E.284, P.285, G.286, R.287, Y.399 Chain B: C.370 Ligands: XAP.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.79, A:G.247, A:G.286, A:R.287, A:Y.399, A:Y.399 Water bridges: A:A.121, A:R.164, A:R.164, A:G.211, A:F.248, A:F.248 Salt bridges: A:H.207 pi-Stacking: A:H.207 PLP.7: 17 residues within 4Å: Chain A: C.370 Chain B: A.77, K.79, D.98, A.121, R.164, L.176, H.207, S.210, G.246, G.247, E.284, P.285, G.286, R.287, Y.399 Ligands: XAP.8 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.77 Hydrogen bonds: B:K.79, B:G.247, B:G.286, B:R.287, B:Y.399, B:Y.399 Water bridges: B:A.121, B:R.164, B:G.211, B:F.248, B:F.248, A:C.370 Salt bridges: B:H.207 pi-Stacking: B:H.207

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

XAP.4: 11 residues within 4Å: Chain A: C.174, L.176, S.210, R.287, Y.341, D.342, Y.399 Chain B: C.370, D.371, F.407 Ligands: PLP.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.399 Hydrogen bonds: A:Y.341, A:D.342 Water bridges: B:D.371, B:D.371 XAP.8: 10 residues within 4Å: Chain A: C.370, D.371, F.407 Chain B: C.174, L.176, S.210, Y.341, D.342, Y.399 Ligands: PLP.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.399 Hydrogen bonds: B:Y.341

2 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)

N2P.5: 7 residues within 4Å: Chain A: G.211, P.249, G.250, S.251, V.254, R.287, N.395 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.249 Hydrogen bonds: A:S.251, A:N.395 Water bridges: A:D.253 N2P.9: 7 residues within 4Å: Chain B: G.211, C.212, T.213, P.249, V.254, K.255, L.256 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.254, B:L.256 Hydrogen bonds: B:L.256 Water bridges: B:C.212, B:G.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dufe, V.T. et al., A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane. Biochem.J. (2007)

Release Date

2007-07-17

Peptides

Ornithine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ornithine decarboxylase