Research workbench
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(PRODUCED from 5-fluoro-6-amino-ump)
Analyse Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MW7
- Type
- protein
- Length
- 515 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
- 5FU
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine 5'-monophosphate synthase (EC 4.1.1.23) | protein | 259 | 43% helix, 18% strand | P11172 |
| B | Uridine 5'-monophosphate synthase (EC 4.1.1.23) | protein | 256 | 45% helix, 18% strand | P11172 |
Ligands and binding sites
- 5FU · 5-fluoro-uridine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 28 | 5FU |
| 2 | 201 | 0.71 | 0.88 | 42 | 5FU |
| 3 | 52 | 0.54 | 0.89 | 15 | empty |
| 4 | 73 | 0.39 | 0.79 | 18 | empty |
| 5 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1943 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3MW7 · 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 3MW7 · PDBe 3MW7 · UniProt P11172
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