Research workbench
2.75 ångström resolution crystal structure of putative orotidine- monophosphate-decarboxylase from toxoplasma gondii.
Analyse 2.75 ångström resolution crystal structure of putative orotidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MJZ
- Type
- protein
- Length
- 580 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
- B9PKU1
- Ligands
- NO3
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 292 | 46% helix, 16% strand | B9PKU1 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 288 | 45% helix, 16% strand | B9PKU1 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.74 | 0.79 | 77 | PEG |
| 2 | 155 | 0.51 | 0.79 | 23 | empty |
| 3 | 139 | 0.50 | 0.79 | 26 | empty |
| 4 | 103 | 0.45 | 0.78 | 19 | empty |
| 5 | 98 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 535 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4MJZ · 2.75 Angstrom Resolution Crystal Structure of Putative… · 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 B9PKU1
- Elsewhere: RCSB PDB 4MJZ · PDBe 4MJZ · UniProt B9PKU1
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