Research workbench
Crystal structure of the class ie ribonucleotide reductase beta subunit from aerococcus urinae in activated form
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
- 6EBP
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase, beta subunit
- EC
- 1.17.4.1
- UniProt
- F2I8X9
- Ligands
- CA
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 303 | 77% helix, 1% strand | F2I8X9 |
| B, D | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 311 | 76% helix, 1% strand | F2I8X9 |
| C | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 304 | 76% helix, 1% strand | F2I8X9 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.56 | 0.82 | 31 | empty |
| 2 | 337 | 0.56 | 0.75 | 50 | GOL |
| 3 | 169 | 0.56 | 0.80 | 35 | empty |
| 4 | 296 | 0.48 | 0.72 | 34 | empty |
| 5 | 157 | 0.48 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2739 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 175 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6EBP · 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 6EBP · PDBe 6EBP · UniProt F2I8X9
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