MolNFT v1 · #46998 · protein
Crystal structure of 5-methylthioribose kinase in complex with ADP-2HO
2OLC: “Crystal structure of 5-methylthioribose kinase in complex with ADP-2HO”. X-ray diffraction, 3 ligands (ADP, CPS, HO), 7 pockets (best druggability 0.79). MolNFT v1 #46998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OLC
- Type
- protein
- Length
- 752 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, HO
- Pockets
- 7 · best druggability 0.79
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 | 376 | 55% helix, 11% strand | O31663 |
| B | Methylthioribose kinase (EC 2.7.1.100) | protein | 376 | 56% helix, 10% 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
- HO · Holmium atom · metal · 4 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 | 139 | 0.79 | 0.96 | 34 | empty |
| 2 | 430 | 0.69 | 0.81 | 38 | empty |
| 3 | 542 | 0.69 | 0.79 | 46 | HO, ADP |
| 4 | 467 | 0.66 | 0.78 | 48 | HO, ADP |
| 5 | 132 | 0.57 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1830 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2OLC · Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho · 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 2OLC · PDBe 2OLC · UniProt O31663
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