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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
- 2PUP
- Type
- protein
- Length
- 741 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
- ADP, CPS, MG, PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioribose kinase (EC 2.7.1.100) | protein | 371 | 54% helix, 12% strand | O31663 |
| B | Methylthioribose kinase (EC 2.7.1.100) | protein | 370 | 56% helix, 11% strand | O31663 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.79 | 0.96 | 32 | empty |
| 2 | 420 | 0.68 | 0.81 | 32 | empty |
| 3 | 454 | 0.66 | 0.78 | 44 | MG, ADP |
| 4 | 359 | 0.60 | 0.77 | 39 | MG, PO4, ADP |
| 5 | 125 | 0.57 | 0.83 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1810 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2PUP · 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 2PUP · PDBe 2PUP · UniProt O31663
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