MolNFT v1 · #152555 · protein
Structure of arabidopsis thaliana ribokinase in unligand form
6ILR: “Structure of arabidopsis thaliana ribokinase in unligand form”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.71). MolNFT v1 #152555 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ILR
- 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
- NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 312 | 35% helix, 24% strand | A1A6H3 |
| B | Ribokinase (EC 2.7.1.15) | protein | 313 | 37% helix, 24% strand | A1A6H3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.71 | 0.79 | 66 | PG4 |
| 2 | 705 | 0.68 | 0.76 | 92 | PG4 |
| 3 | 109 | 0.38 | 0.74 | 24 | empty |
| 4 | 55 | 0.33 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1319 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 6ILR · PDBe 6ILR · UniProt A1A6H3
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