MolNFT v1 · #48476 · protein
Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding
2PUL: “Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding”. X-ray diffraction, 3 ligands (ACP, CPS, MG), 8 pockets (best druggability 0.80). MolNFT v1 #48476 on GenesisL1: 3D…
- PDB
- 2PUL
- Type
- protein
- Length
- 750 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, CPS, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioribose kinase (EC 2.7.1.100) | protein | 381 | 56% helix, 11% strand | O31663 |
| B | Methylthioribose kinase (EC 2.7.1.100) | protein | 369 | 57% helix, 11% strand | O31663 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.80 | 0.97 | 31 | empty |
| 2 | 607 | 0.70 | 0.78 | 48 | MG, ACP |
| 3 | 454 | 0.70 | 0.81 | 35 | empty |
| 4 | 489 | 0.66 | 0.78 | 49 | MG, ACP |
| 5 | 145 | 0.57 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1773 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2PUL · 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 2PUL · PDBe 2PUL · UniProt O31663
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