Research workbench
Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase from E. COLI causes a change in crystal contacts and space group
Analyse Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JJK
- Type
- protein
- Length
- 3,696 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- P08244
- Ligands
- BMP
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 231 | 49% helix, 17% strand | P08244 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.76 | 0.93 | 35 | BMP |
| 2 | 73 | 0.75 | 0.98 | 24 | empty |
| 3 | 814 | 0.75 | 0.79 | 55 | empty |
| 4 | 448 | 0.74 | 0.84 | 53 | empty |
| 5 | 147 | 0.74 | 0.92 | 37 | BMP |
Interfaces
30 interfaces between chains.
- M–N · 2157 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2140 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2139 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2137 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2134 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 128 modified (engineered).
Compared structures
- 1JJK · Selenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli… · the same entry in another collection · chain P against P, 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 P08244
- Elsewhere: RCSB PDB 1JJK · PDBe 1JJK · UniProt P08244
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.