Research workbench
Vibrio cholerae O395 ribokinase complexed with ribose, ADP and sodium ion.
Analyse Vibrio cholerae O395 ribokinase complexed with ribose, ADP and sodium ion. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDA
- 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, NA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribokinase (EC 2.7.1.15) | protein | 306 | 39% helix, 26% strand | A5F1B7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D
- RIB · alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C, D
- NA · Sodium 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.75 | 0.80 | 95 | ADP |
| 2 | 456 | 0.74 | 0.84 | 57 | RIB, ADP |
| 3 | 1041 | 0.74 | 0.77 | 112 | RIB, ADP |
| 4 | 428 | 0.73 | 0.83 | 51 | RIB, ADP |
| 5 | 104 | 0.46 | 0.79 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1336 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1321 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 429 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XDA · Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium 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 4XDA · PDBe 4XDA · UniProt A5F1B7
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