MolNFT v1 · #12604 · protein
Crystal structure of orotidine monophosphate decarboxylase mutant D70N complexed with 6-azaump
1KM0 · Orotidine 5'-phosphate decarboxylase: “Crystal structure of orotidine monophosphate decarboxylase mutant D70N complexed with 6-azaump”. X-ray diffraction, 1 ligand (UP6), 9 pockets (best druggability 0.80). MolNFT v1 #12604 on…
- PDB
- 1KM0
- Type
- protein
- Length
- 898 residues
- Chains
- 4
- 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
- UP6
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 237 | 52% helix, 17% strand | O26232 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 212 | 49% helix, 19% strand | O26232 |
| C | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 235 | 52% helix, 17% strand | O26232 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 214 | 50% helix, 19% strand | O26232 |
Ligands and binding sites
- UP6 · 6-aza uridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.80 | 0.97 | 34 | UP6 |
| 2 | 127 | 0.78 | 0.96 | 31 | UP6 |
| 3 | 132 | 0.78 | 0.96 | 34 | UP6 |
| 4 | 128 | 0.78 | 0.96 | 34 | UP6 |
| 5 | 462 | 0.67 | 0.79 | 60 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1732 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1727 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1KM0 · Crystal structure of orotidine monophosphate decarboxylase mutant D70N 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 O26232
- Elsewhere: RCSB PDB 1KM0 · PDBe 1KM0 · UniProt O26232
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