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Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: datp-cdp complex
Analyse Structural mechanism of allosteric substrate specificity in a ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XJN
- Type
- protein
- Length
- 2,450 residues
- Chains
- 4
- 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
- CDP, DTP, CL
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 618 | 46% helix, 13% strand | O33839 |
| B | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 610 | 45% helix, 13% strand | O33839 |
| C | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 615 | 46% helix, 13% strand | O33839 |
| D | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 607 | 45% helix, 14% strand | O33839 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.76 | 0.79 | 137 | CDP |
| 2 | 830 | 0.76 | 0.80 | 92 | CL, CDP |
| 3 | 782 | 0.73 | 0.78 | 72 | DTP, CDP |
| 4 | 621 | 0.72 | 0.80 | 62 | CDP |
| 5 | 490 | 0.72 | 0.81 | 49 | DTP |
Interfaces
2 interfaces between chains.
- A–B · 1291 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1279 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1XJN · Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase… · the same entry in another collection · chain B against B, 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 1XJN · PDBe 1XJN · UniProt O33839
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