MolNFT v1 · #109770 · protein
Vibrio cholerae O395 ribokinase complexed with ADP, ribose and cesium ion.
4XCK: “Vibrio cholerae O395 ribokinase complexed with ADP, ribose and cesium ion.”. X-ray diffraction, 3 ligands (ADP, RIB, CS), 9 pockets (best druggability 0.76). MolNFT v1 #109770 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4XCK
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- A5F1B7
- Ligands
- ADP, RIB, CS
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribokinase (EC 2.7.1.15) | protein | 306 | 40% helix, 25% strand | A5F1B7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D
- RIB · alpha-D-ribofuranose · ligand · 2 copies · chains A, B, C, D
- CS · Cesium 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.76 | 0.80 | 103 | ADP |
| 2 | 934 | 0.73 | 0.77 | 106 | ADP |
| 3 | 390 | 0.72 | 0.84 | 52 | RIB, ADP |
| 4 | 341 | 0.70 | 0.84 | 40 | ADP |
| 5 | 149 | 0.41 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1325 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1313 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 457 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XCK · Vibrio cholerae O395 Ribokinase complexed with ADP, Ribose and Cesium ion. · 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 A5F1B7
- Elsewhere: RCSB PDB 4XCK · PDBe 4XCK · UniProt A5F1B7
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