MolNFT v1 · #55907 · protein
Crystal structure of uncharacterized conserved protein from geobacillus kaustophilus
2YYU · Orotidine 5'-phosphate decarboxylase: “Crystal structure of uncharacterized conserved protein from geobacillus kaustophilus”. X-ray diffraction, 1 ligand (C5P), 3 pockets (best druggability 0.72). MolNFT v1 #55907 on GenesisL1: 3D…
- PDB
- 2YYU
- Type
- protein
- Length
- 454 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
- Q5L0U0
- Ligands
- C5P
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 225 | 50% helix, 16% strand | Q5L0U0 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 229 | 49% helix, 17% strand | Q5L0U0 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 26 | empty |
| 2 | 382 | 0.70 | 0.82 | 47 | C5P |
| 3 | 423 | 0.67 | 0.79 | 50 | C5P |
Interfaces
1 interface between chains.
- A–B · 1902 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2YYU · Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5L0U0 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q5L0U0) · 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 Q5L0U0
- Elsewhere: RCSB PDB 2YYU · PDBe 2YYU · UniProt Q5L0U0
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