Research workbench
E. COLI ribokinase complexed with ribose and ADP, solved in space group P212121
Analyse E. COLI ribokinase complexed with ribose and ADP, solved in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RK2
- Type
- protein
- Length
- 1,223 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- P0A9J6
- Ligands
- RIB, ALF, ADP, MG
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribokinase (EC 2.7.1.15) | protein | 305 | 40% helix, 25% strand | P0A9J6 |
| B | Ribokinase (EC 2.7.1.15) | protein | 307 | 39% helix, 25% strand | P0A9J6 |
| C | Ribokinase (EC 2.7.1.15) | protein | 306 | 40% helix, 25% strand | P0A9J6 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
- ALF · Tetrafluoroaluminate ion · ligand · 4 copies · chains A, B, D, C
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.76 | 0.78 | 63 | ALF |
| 2 | 439 | 0.72 | 0.83 | 51 | RIB, ADP |
| 3 | 469 | 0.72 | 0.82 | 52 | RIB, ADP |
| 4 | 485 | 0.72 | 0.82 | 52 | RIB, ADP |
| 5 | 483 | 0.71 | 0.81 | 52 | RIB, ADP |
Interfaces
3 interfaces between chains.
- C–D · 1184 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1124 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1RK2 · E. COLI ribokinase complexed with ribose and ADP, solved in space group P212121 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9J6 · AlphaFold monomer V2.0 prediction for ribokinase (P0A9J6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0A9J6
- Elsewhere: RCSB PDB 1RK2 · PDBe 1RK2 · UniProt P0A9J6
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