Research workbench
Crystal structure of ribokinase in complex with ATP and glycerol in the active site from klebsiella pneumoniae
Analyse Crystal structure of ribokinase in complex with ATP and glycerol in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKH
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate kinase
- EC
- 2.7.1.15
- UniProt
- A6T989
- Ligands
- ATP
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Carbohydrate kinase (EC 2.7.1.15) | protein | 286 | 37% helix, 23% strand | A6T989 |
| B | Carbohydrate kinase (EC 2.7.1.15) | protein | 283 | 37% helix, 25% strand | A6T989 |
| C | Carbohydrate kinase (EC 2.7.1.15) | protein | 285 | 38% helix, 25% strand | A6T989 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.74 | 0.80 | 95 | empty |
| 2 | 497 | 0.74 | 0.83 | 56 | ATP, GOL |
| 3 | 495 | 0.73 | 0.82 | 54 | ATP, GOL |
| 4 | 171 | 0.55 | 0.80 | 33 | ATP |
| 5 | 145 | 0.53 | 0.81 | 29 | ATP |
Interfaces
5 interfaces between chains.
- B–D · 1449 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1362 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3IKH · Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from… · 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 A6T989
- Elsewhere: RCSB PDB 3IKH · PDBe 3IKH · UniProt A6T989
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