MolNFT v1 · #33918 · protein
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii OT3 at 1.6 a resolution
2CZD: “Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii OT3 at 1.6 a resolution”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #33918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2CZD
- Type
- protein
- Length
- 413 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
- O58462
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 206 | 50% helix, 18% strand | O58462 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 207 | 49% helix, 18% strand | O58462 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.63 | 0.80 | 38 | DTT |
| 2 | 228 | 0.58 | 0.79 | 30 | empty |
| 3 | 63 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1531 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2CZD · Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3… · the same entry in another collection · chain A against A, TM-score 1.00
- O58462 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (O58462) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O58462
- Elsewhere: RCSB PDB 2CZD · PDBe 2CZD · UniProt O58462
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