MolNFT v1 · #83004 · protein
Myo-inositol kinase from thermococcus kodakarensis
3W4S · CARBOHYDRATE/PYRIMIDINE kinase, pfkb family: “Myo-inositol kinase from thermococcus kodakarensis”. X-ray diffraction, 1 ligand (IOD), 4 pockets (best druggability 0.74). MolNFT v1 #83004 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3W4S
- Type
- protein
- Length
- 541 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CARBOHYDRATE/PYRIMIDINE kinase, pfkb family
- UniProt
- Q5JDA3
- Ligands
- IOD
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CARBOHYDRATE/PYRIMIDINE kinase, pfkb family | protein | 273 | 31% helix, 32% strand | Q5JDA3 |
| B | CARBOHYDRATE/PYRIMIDINE kinase, pfkb family | protein | 268 | 31% helix, 33% strand | Q5JDA3 |
Ligands and binding sites
- IOD · Iodide ion · ion · 30 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 | 536 | 0.74 | 0.82 | 55 | IOD |
| 2 | 513 | 0.73 | 0.82 | 50 | IOD |
| 3 | 91 | 0.35 | 0.74 | 22 | IOD |
| 4 | 78 | 0.29 | 0.72 | 17 | IOD |
Interfaces
1 interface between chains.
- A–B · 688 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3W4S · Myo-inositol kinase from Thermococcus kodakarensis · 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 Q5JDA3
- Elsewhere: RCSB PDB 3W4S · PDBe 3W4S · UniProt Q5JDA3
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