Research workbench
Crystal structure of L-ribulose-5-phosphate 4-epimerase
Analyse Crystal structure of L-ribulose-5-phosphate 4-epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K0W
- Type
- protein
- Length
- 1,338 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribulose 5 phosphate 4-epimerase
- EC
- 5.1.3.4
- UniProt
- P08203
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | L-ribulose 5 phosphate 4-epimerase (EC 5.1.3.4) | protein | 223 | 43% helix, 16% strand | P08203 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.36 | 0.78 | 16 | empty |
| 2 | 65 | 0.34 | 0.77 | 15 | empty |
| 3 | 55 | 0.34 | 0.78 | 18 | empty |
| 4 | 61 | 0.33 | 0.77 | 18 | empty |
| 5 | 60 | 0.31 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–E · 27 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 17 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1K0W · Crystal structure of L-ribulose-5-phosphate 4-epimerase · the same entry in another collection · chain F against F, TM-score 1.00
- P08203 · AlphaFold monomer V2.0 prediction for L-ribulose-5-phosphate 4-epimerase arad (P08203) · a predicted model of the same protein · chain D 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 P08203
- Elsewhere: RCSB PDB 1K0W · PDBe 1K0W · UniProt P08203
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