Research workbench
Crystal structure of a putative ribokinase in complex with ADP from E.COLI
Analyse Crystal structure of a putative ribokinase in complex with ADP from E.COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IN1
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized sugar kinase ydjh
- EC
- 2.7.1.-
- UniProt
- P77493
- Ligands
- ADP, NA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized sugar kinase ydjh (EC 2.7.1.-) | protein | 312 | 38% helix, 23% strand | P77493 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.69 | 0.77 | 62 | ADP, NA |
| 2 | 630 | 0.69 | 0.77 | 66 | ADP, NA |
Interfaces
1 interface between chains.
- A–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3IN1 · Crystal structure of a putative Ribokinase in complex with ADP from E.coli · the same entry in another collection · chain A against A, TM-score 1.00
- P77493 · AlphaFold monomer V2.0 prediction for uncharacterized sugar kinase ydjh (P77493) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P77493
- Elsewhere: RCSB PDB 3IN1 · PDBe 3IN1 · UniProt P77493
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