MolNFT v1 · #57062 · protein
Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with 6-cyano-ump
2ZZ4 · Orotidine 5'-phosphate decarboxylase: “Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with…”. X-ray diffraction, 1 ligand (6CN), 2 pockets (best druggability 0.73). MolNFT v1 #57062…
- PDB
- 2ZZ4
- Type
- protein
- Length
- 430 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
- 6CN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 215 | 51% helix, 19% strand | O26232 |
Ligands and binding sites
- 6CN · 6-cyanouridine 5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · 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 | 93 | 0.73 | 0.95 | 31 | 6CN |
| 2 | 101 | 0.72 | 0.94 | 28 | 6CN |
Interfaces
1 interface between chains.
- A–B · 1735 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2ZZ4 · Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M.… · 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 2ZZ4 · PDBe 2ZZ4 · UniProt O26232
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