Research workbench
Ribonucleotide reductase R2 subunit from clostridium botulinum
Analyse Ribonucleotide reductase R2 subunit from clostridium botulinum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZJK
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- B1KYY8
- Ligands
- FE
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 316 | 70% helix, 1% strand | B1KYY8 |
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 317 | 70% helix, 1% strand | B1KYY8 |
| D | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 315 | 70% helix, 1% strand | B1KYY8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains C, A, D, B
- GOL · Glycerol · additive · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.72 | 0.99 | 20 | empty |
| 2 | 737 | 0.70 | 0.77 | 58 | empty |
| 3 | 64 | 0.47 | 0.83 | 18 | empty |
| 4 | 58 | 0.47 | 0.84 | 15 | empty |
| 5 | 72 | 0.46 | 0.82 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2925 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2897 Ų buried · 61 hydrogen bonds · protein-protein
- C–A · 544 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZJK · Ribonucleotide reductase R2 subunit from Clostridium botulinum · the same entry in another collection · chain C against C, 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 B1KYY8
- Elsewhere: RCSB PDB 6ZJK · PDBe 6ZJK · UniProt B1KYY8
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