MolNFT v1 · #13819 · protein
Crystal structure of orotidine monophosphate decarboxylase mutant DELTAR203A complexed with 6-azaump
1LOS: “Crystal structure of orotidine monophosphate decarboxylase mutant DELTAR203A complexed with 6-azaump”. X-ray diffraction, 1 ligand (UP6), 7 pockets (best druggability 0.77). MolNFT v1 #13819 on GenesisL1: 3D structure, binding sites…
- PDB
- 1LOS
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine monophosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- UP6
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine monophosphate decarboxylase (EC 4.1.1.23) | protein | 216 | 49% helix, 19% strand | O26232 |
| B | Orotidine monophosphate decarboxylase (EC 4.1.1.23) | protein | 206 | 48% helix, 19% strand | O26232 |
| C | Orotidine monophosphate decarboxylase (EC 4.1.1.23) | protein | 191 | 48% helix, 21% strand | O26232 |
| D | Orotidine monophosphate decarboxylase (EC 4.1.1.23) | protein | 214 | 48% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.77 | 0.79 | 101 | empty |
| 2 | 248 | 0.64 | 0.82 | 41 | UP6 |
| 3 | 232 | 0.64 | 0.82 | 41 | UP6 |
| 4 | 231 | 0.63 | 0.82 | 37 | UP6 |
| 5 | 227 | 0.62 | 0.81 | 40 | UP6 |
Interfaces
3 interfaces between chains.
- C–D · 1586 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1576 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1LOS · crystal structure of orotidine monophosphate decarboxylase mutant deltaR203A complexed… · 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 1LOS · PDBe 1LOS · UniProt O26232
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