Research workbench
Crystal structure of a putative ribokinase II in complex with ATP and MG+2 from E.COLI
Analyse Crystal structure of a putative ribokinase II in complex with ATP and MG+2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IQ0
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ribokinase II
- EC
- 2.7.1.-
- UniProt
- Q8FD38
- Ligands
- ATP, MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ribokinase II (EC 2.7.1.-) | protein | 307 | 41% helix, 25% strand | Q8FD38 |
| B | Putative ribokinase II (EC 2.7.1.-) | protein | 308 | 38% helix, 23% strand | Q8FD38 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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 | 741 | 0.73 | 0.79 | 64 | MG, ATP |
| 2 | 676 | 0.70 | 0.78 | 61 | MG, ATP |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3IQ0 · Crystal structure of a putative Ribokinase II in complex with ATP and Mg+2 from E.coli · 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 Q8FD38
- Elsewhere: RCSB PDB 3IQ0 · PDBe 3IQ0 · UniProt Q8FD38
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