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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
- 2PUN
- Type
- protein
- Length
- 758 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
- ACP, SR1, CPS, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioribose kinase (EC 2.7.1.100) | protein | 380 | 54% helix, 11% strand | O31663 |
| B | Methylthioribose kinase (EC 2.7.1.100) | protein | 378 | 54% helix, 11% strand | O31663 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- SR1 · 5-S-methyl-5-thio-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 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 | 33 | empty |
| 2 | 595 | 0.69 | 0.78 | 50 | MG, ACP, SR1 |
| 3 | 447 | 0.68 | 0.80 | 38 | empty |
| 4 | 480 | 0.64 | 0.77 | 44 | MG, SR1, ACP |
| 5 | 131 | 0.59 | 0.84 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PUN · 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 2PUN · PDBe 2PUN · UniProt O31663
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