Research workbench
1.8 ångström resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrf) from campylobacter jejuni subsp. jejuni nctc 11168
Analyse 1.8 ångström resolution crystal structure of orotidine 5'-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RU6
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- Q9PIC1
- Ligands
- IOD, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 220 | 47% helix, 17% strand | Q9PIC1 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 222 | 46% helix, 18% strand | Q9PIC1 |
| C | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 218 | 48% helix, 17% strand | Q9PIC1 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 218 | 48% helix, 17% strand | Q9PIC1 |
Ligands and binding sites
- IOD · Iodide ion · ion · 26 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.67 | 0.81 | 47 | IOD |
| 2 | 282 | 0.66 | 0.82 | 41 | IOD |
| 3 | 292 | 0.65 | 0.81 | 40 | IOD |
| 4 | 301 | 0.64 | 0.80 | 43 | IOD |
Interfaces
2 interfaces between chains.
- A–D · 1751 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1742 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3RU6 · 1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PIC1 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q9PIC1) · a predicted model of the same protein · chain D 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 Q9PIC1
- Elsewhere: RCSB PDB 3RU6 · PDBe 3RU6 · UniProt Q9PIC1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.