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Crystal structure of Ribokinase in Complex with D-Ribose from Klebsiella pneumoniae
Analyse Crystal structure of Ribokinase in Complex with D-Ribose from Klebsiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I3Y
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Klebsiella pneumoniae subsp. pneumoniae MGH 78578
- Molecule
- Carbohydrate kinase
- EC
- 2.7.1.15
- UniProt
- A6T989
- Ligands
- RIB, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.15 · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Carbohydrate kinase (EC 2.7.1.15) | protein | 285 | 33% helix, 23% strand | A6T989 |
| B | Carbohydrate kinase (EC 2.7.1.15) | protein | 282 | 34% helix, 24% strand | A6T989 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · sugar · chains D
- SO4 · Sulfate ion · ion · 6 copies · chains B, D, C
- GOL · Glycerol · additive · chains C
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 | 489 | 0.74 | 0.83 | 56 | SO4, GOL |
| 2 | 498 | 0.74 | 0.83 | 53 | SO4, RIB |
| 3 | 746 | 0.71 | 0.78 | 72 | empty |
| 4 | 514 | 0.64 | 0.76 | 73 | empty |
| 5 | 320 | 0.55 | 0.76 | 39 | SO4 |
Interfaces
5 interfaces between chains.
- B–D · 1458 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1368 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 547 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3I3Y · Crystal structure of ribokinase in complex with D-ribose from klebsiella pneumoniae · 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 3I3Y · PDBe 3I3Y · UniProt A6T989
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