Research workbench
Mn-containing form of the ribonucleotide reductase nrdb protein from leeuwenhoekiella blandensis
Analyse Mn-containing form of the ribonucleotide reductase nrdb protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SF5
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase, beta subunit 1
- EC
- 1.17.4.1
- UniProt
- A3XHF9
- Ligands
- MN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase, beta subunit 1 (EC 1.17.4.1) | protein | 296 | 75% helix, 1% strand | A3XHF9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.72 | 0.86 | 62 | empty |
| 2 | 659 | 0.70 | 0.77 | 52 | empty |
| 3 | 650 | 0.68 | 0.77 | 52 | empty |
| 4 | 97 | 0.60 | 0.87 | 20 | empty |
| 5 | 82 | 0.55 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6SF5 · Mn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella… · 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 A3XHF9
- Elsewhere: RCSB PDB 6SF5 · PDBe 6SF5 · UniProt A3XHF9
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