Research workbench
Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, inactive form
Analyse Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, inactive form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GP3
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.23
- Source
- Mesoplasma florum (strain ATCC 33453 / NBRC 100688 / NCTC 11704 / L1)
- Molecule
- Ribonucleoside-diphosphate reductase beta chain
- UniProt
- Q6F0T5
- Ligands
- CA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · resolution 1.23 · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase beta chain | protein | 318 | 74% helix, 1% strand | Q6F0T5 |
| B | Ribonucleoside-diphosphate reductase beta chain | protein | 313 | 75% helix, 1% strand | Q6F0T5 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.60 | 0.76 | 29 | empty |
| 2 | 138 | 0.45 | 0.76 | 24 | empty |
| 3 | 62 | 0.34 | 0.77 | 16 | empty |
| 4 | 79 | 0.30 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2757 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6GP3 · Ribonucleotide reductase class ie R2 from mesoplasma florum, inactive form · 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 Q6F0T5
- Elsewhere: RCSB PDB 6GP3 · PDBe 6GP3 · UniProt Q6F0T5
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