Research workbench
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6- dihydroorotidine 5'-monophosphate
Analyse Crystal structure 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
- 3G1F
- Type
- protein
- Length
- 2,815 residues
- Chains
- 13
- 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
- 2OM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 220 | 49% helix, 19% strand | O26232 |
| B, H, K, L | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 216 | 46% helix, 19% strand | O26232 |
| C, J | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 218 | 48% helix, 19% strand | O26232 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 215 | 49% helix, 19% strand | O26232 |
| E, F, G, M | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 217 | 45% helix, 17% strand | O26232 |
| I | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 212 | 46% helix, 18% strand | O26232 |
Ligands and binding sites
- 2OM · 5,6-dihydroorotidine 5'-monophosphate · ligand · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M
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 | 308 | 0.86 | 0.96 | 76 | 2OM |
| 2 | 196 | 0.82 | 0.96 | 47 | 2OM |
| 3 | 181 | 0.81 | 0.96 | 47 | 2OM |
| 4 | 184 | 0.81 | 0.96 | 41 | 2OM |
| 5 | 159 | 0.81 | 0.96 | 41 | 2OM |
Interfaces
13 interfaces between chains.
- E–F · 1724 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1713 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1707 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1688 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 1657 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3G1F · Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium… · 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 3G1F · PDBe 3G1F · UniProt O26232
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