MolNFT v1 · #152557 · protein
Structure of arabidopsis thaliana ribokinase complexed with ATP and magnesium ion
6ILT: “Structure of arabidopsis thaliana ribokinase complexed with ATP and magnesium ion”. X-ray diffraction, 3 ligands (ATP, MG, NA), 5 pockets (best druggability 0.69). MolNFT v1 #152557 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ILT
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- A1A6H3
- Ligands
- ATP, MG, NA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 312 | 36% helix, 25% strand | A1A6H3 |
| B | Ribokinase (EC 2.7.1.15) | protein | 313 | 37% helix, 25% strand | A1A6H3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.69 | 0.77 | 88 | ATP, MG |
| 2 | 594 | 0.68 | 0.77 | 65 | ATP, MG |
| 3 | 85 | 0.37 | 0.76 | 22 | empty |
| 4 | 77 | 0.36 | 0.77 | 19 | empty |
| 5 | 70 | 0.29 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6ILT · Structure of Arabidopsis thaliana Ribokinase complexed with ATP and Magnesium ion · the same entry in another collection · chain A against A, TM-score 1.00
- A1A6H3 · AlphaFold monomer V2.0 prediction for ribokinase (A1A6H3) · a predicted model of the same protein · chain B 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 A1A6H3
- Elsewhere: RCSB PDB 6ILT · PDBe 6ILT · UniProt A1A6H3
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