MolNFT v1 · #20610 · protein
E. COLI ribokinase complexed with ribose and ADP, solved in space group P212121
1RK2: “E. COLI ribokinase complexed with ribose and ADP, solved in space group P212121”. X-ray diffraction, 4 ligands (RIB, ALF, ADP), 10 pockets (best druggability 0.76). MolNFT v1 #20610 on GenesisL1: 3D structure, binding sites and…
- 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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