MolNFT v1 · #187160 · protein
Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center
7S3G: “Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at…”. X-ray diffraction, 1 ligand (PLP), 17 pockets (best druggability 0.75). MolNFT v1 #187160 on GenesisL1: 3D structure…
- PDB
- 7S3G
- Type
- protein
- Length
- 803 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- P11926
- Ligands
- PLP
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 402 | 38% helix, 24% strand | P11926 |
| B | Ornithine decarboxylase (EC 4.1.1.17) | protein | 401 | 38% helix, 24% strand | P11926 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.75 | 0.83 | 56 | PLP, CIT |
| 2 | 331 | 0.66 | 0.80 | 35 | empty |
| 3 | 253 | 0.66 | 0.83 | 41 | PLP, CIT |
| 4 | 333 | 0.66 | 0.80 | 30 | empty |
| 5 | 191 | 0.56 | 0.80 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2575 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7S3G · Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in… · the same entry in another collection · chain A against A, TM-score 1.00
- P11926 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P11926) · a predicted model of the same protein · chain A against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 7S3G · PDBe 7S3G · UniProt P11926
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