Research workbench
Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding
Analyse Structures of 5-methylthioribose kinase reveal substrate specificity and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PU8
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioribose kinase
- EC
- 2.7.1.100
- UniProt
- O31663
- Ligands
- CPS
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioribose kinase (EC 2.7.1.100) | protein | 373 | 55% helix, 11% strand | O31663 |
| B | Methylthioribose kinase (EC 2.7.1.100) | protein | 365 | 59% helix, 10% strand | O31663 |
Ligands and binding sites
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.72 | 0.97 | 20 | empty |
| 2 | 61 | 0.71 | 0.97 | 16 | empty |
| 3 | 449 | 0.70 | 0.81 | 41 | empty |
| 4 | 552 | 0.69 | 0.78 | 47 | empty |
| 5 | 284 | 0.58 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1813 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2PU8 · Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of… · the same entry in another collection · chain A against A, TM-score 1.00
- O31663 · AlphaFold monomer V2.0 prediction for methylthioribose kinase (O31663) · a predicted model of the same protein · chain B 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 O31663
- Elsewhere: RCSB PDB 2PU8 · PDBe 2PU8 · UniProt O31663
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.