MolNFT v1 · #27425 · protein
Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: datp complex
1XJF · Ribonucleotide reductase, B12-dependent: “Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: datp complex”. X-ray diffraction, 2 ligands (DTP, MG), 8 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 1XJF
- Type
- protein
- Length
- 1,230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase, B12-dependent
- EC
- 1.17.4.1
- UniProt
- O33839
- Ligands
- DTP, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 619 | 46% helix, 12% strand | O33839 |
| B | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 611 | 47% helix, 11% strand | O33839 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B
- 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 | 1131 | 0.75 | 0.78 | 126 | empty |
| 2 | 577 | 0.67 | 0.77 | 64 | empty |
| 3 | 86 | 0.62 | 0.89 | 19 | DTP |
| 4 | 95 | 0.60 | 0.88 | 21 | DTP |
| 5 | 311 | 0.57 | 0.77 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1389 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1XJF · Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase… · the same entry in another collection · chain A against A, TM-score 1.00
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 O33839
- Elsewhere: RCSB PDB 1XJF · PDBe 1XJF · UniProt O33839
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