Research workbench
Crystal structure of the class ie ribonucleotide reductase beta subunit from aerococcus urinae with CU(I) bound (cu sulfate soak)
Analyse Crystal structure of the class ie ribonucleotide reductase beta subunit from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MMV
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- F2I8X9
- Ligands
- CU1, CL
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 309 | 77% helix, 1% strand | F2I8X9 |
| B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 313 | 76% helix, 1% strand | F2I8X9 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.50 | 0.79 | 35 | empty |
| 2 | 100 | 0.40 | 0.76 | 17 | empty |
| 3 | 54 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2758 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7MMV · Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus… · 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 F2I8X9
- Elsewhere: RCSB PDB 7MMV · PDBe 7MMV · UniProt F2I8X9
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