MolNFT v1 · #101492 · protein
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 3-deazauridine 5'-monophosphate
4NT0 · Orotidine 5'-phosphate decarboxylase: “Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum…”. X-ray diffraction, 2 ligands (3DU, CA), 2 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 4NT0
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- 3DU, CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 213 | 49% helix, 18% strand | O26232 |
Ligands and binding sites
- 3DU · 4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.70 | 0.85 | 42 | 3DU |
| 2 | 230 | 0.65 | 0.83 | 30 | 3DU |
Interfaces
1 interface between chains.
- A–B · 1690 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4NT0 · Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
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 O26232
- Elsewhere: RCSB PDB 4NT0 · PDBe 4NT0 · UniProt O26232
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