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Crystal structure of trypanosoma brucei ornithine decarboxylase

Analyse Crystal structure of trypanosoma brucei ornithine decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QU4
Type: protein
Length: 1,424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ornithine decarboxylase
EC: 4.1.1.17
UniProt: P07805
Ligands: PLP
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ornithine decarboxylase (EC 4.1.1.17)	protein	356	35% helix, 25% strand	P07805

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	479	0.73	0.82	67	PLP
2	471	0.73	0.82	61	PLP
3	507	0.72	0.81	67	PLP
4	203	0.67	0.85	32	PLP
5	293	0.59	0.78	35	empty

Interfaces

2 interfaces between chains.

A–B · 2527 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 2522 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1QU4 · Crystal structure of trypanosoma brucei ornithine decarboxylase · the same entry in another collection · chain D against D, TM-score 1.00
P07805 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P07805) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P07805
Elsewhere: RCSB PDB 1QU4 · PDBe 1QU4 · UniProt P07805

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