SMTL ID : 1njj.1 (1 other biounit)

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x GET: GENETICIN(Non-covalent)

GET.1: 8 residues within 4Å: Chain A: R.22, D.243, L.339, P.340, Q.341, L.382, E.384, D.385 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.339, A:Q.341, A:L.382 Hydrogen bonds: A:R.22, A:D.243, A:E.384, A:E.384 Water bridges: A:T.21, A:P.340 GET.3: 13 residues within 4Å: Chain B: R.22, C.26, R.242, D.243, R.337, L.339, P.340, Q.341, R.342, E.343, L.382, E.384, D.385 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.242, B:E.343 Hydrogen bonds: B:D.243, B:E.384, B:E.384, B:D.385

2 x ORX: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE(Non-covalent)

ORX.2: 19 residues within 4Å: Chain A: A.67, K.69, D.88, R.154, H.197, G.236, G.237, F.238, E.274, P.275, G.276, R.277, Y.331, D.332, Y.389 Chain B: Y.323, C.360, D.361, G.362 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.237, A:F.238, A:E.274, A:G.276, A:R.277, A:D.332, A:Y.389, B:C.360, B:G.362 Water bridges: A:R.154, A:Y.278 Salt bridges: A:H.197, A:R.277 pi-Cation interactions: A:K.69, A:H.197 ORX.4: 17 residues within 4Å: Chain A: Y.323, C.360, D.361 Chain B: A.67, K.69, D.88, R.154, H.197, G.236, G.237, F.238, E.274, G.276, R.277, Y.331, D.332, Y.389 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.69 Hydrogen bonds: B:G.237, B:F.238, B:G.276, B:R.277, B:D.332, B:Y.389, A:Y.323, A:C.360, A:C.360 Salt bridges: B:H.197, B:R.277 pi-Cation interactions: B:K.69, B:H.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, L.K. et al., X-ray Structure Determination of Trypanosoma brucei Ornithine Decarboxylase Bound to D-Ornithine and to G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL FLEXIBILITY. J.Biol.Chem. (2003)

Release Date

2003-08-26

Peptides

ornithine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ornithine decarboxylase

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