Research workbench
Crystal structure of odc-plp-AZ1 ternary complex
Analyse Crystal structure of odc-plp-AZ1 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BWA
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase; Ornithine decarboxylase antizyme 1
- EC
- 4.1.1.17
- UniProt
- P11926, P54368
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 350 | 34% helix, 23% strand | P11926 |
| B | Ornithine decarboxylase antizyme 1 | protein | 121 | 16% helix, 36% strand | P54368 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.81 | 0.83 | 105 | PLP |
| 2 | 230 | 0.57 | 0.79 | 25 | empty |
| 3 | 56 | 0.42 | 0.82 | 16 | empty |
| 4 | 69 | 0.35 | 0.77 | 15 | empty |
| 5 | 69 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1790 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5BWA · Crystal structure of ODC-PLP-AZ1 ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P54368 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase antizyme 1 (P54368) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P11926 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P11926) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P11926
- Every structure of UniProt P54368
- Elsewhere: RCSB PDB 5BWA · PDBe 5BWA · UniProt P11926 · UniProt P54368
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