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Crystal structure of orotidine 5'-phosphate decarboxylase from klebsiella pneumoniae in complex with uridine-5'-monophosphate
Analyse Crystal structure of orotidine 5'-phosphate decarboxylase from klebsiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CSO
- Type
- protein
- Length
- 2,191 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- A0A0H3GNE4
- Ligands
- U5P
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 229 | 48% helix, 17% strand | A0A0H3GNE4 |
| C | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 231 | 48% helix, 17% strand | A0A0H3GNE4 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 221 | 50% helix, 18% strand | A0A0H3GNE4 |
| E, F | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 231 | 49% helix, 17% strand | A0A0H3GNE4 |
| G | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 206 | 51% helix, 18% strand | A0A0H3GNE4 |
| H | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 212 | 50% helix, 18% strand | A0A0H3GNE4 |
| I | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 217 | 51% helix, 18% strand | A0A0H3GNE4 |
| J | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 184 | 51% helix, 16% strand | A0A0H3GNE4 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, E, F
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 | 97 | 0.78 | 0.98 | 27 | empty |
| 2 | 124 | 0.78 | 0.96 | 31 | empty |
| 3 | 91 | 0.78 | 0.98 | 26 | empty |
| 4 | 91 | 0.78 | 0.98 | 19 | empty |
| 5 | 99 | 0.77 | 0.97 | 29 | U5P |
Interfaces
10 interfaces between chains.
- A–B · 2153 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1937 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1826 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1688 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1320 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 8CSO · Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in… · 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 A0A0H3GNE4
- Elsewhere: RCSB PDB 8CSO · PDBe 8CSO · UniProt A0A0H3GNE4
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