MolNFT v1 · #71568 · protein
Crystal structure of human orotidine-5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate
3MI2 · Uridine 5'-monophosphate synthase: “Crystal structure of human orotidine-5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate”. X-ray diffraction, 1 ligand (PFU), 3 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3MI2
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- PFU
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine 5'-monophosphate synthase (EC 4.1.1.23) | protein | 257 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- PFU · (1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.76 | 0.94 | 30 | PFU |
| 2 | 117 | 0.74 | 0.94 | 32 | PFU |
| 3 | 63 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1949 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3MI2 · Crystal structure of human orotidine-5'-monophosphate decarboxylase complexed with… · 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 P11172
- Elsewhere: RCSB PDB 3MI2 · PDBe 3MI2 · UniProt P11172
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