Research workbench
R2-like ligand-binding oxidase Y162F mutant with aerobically reconstituted MN/FE cofactor
Analyse R2-like ligand-binding oxidase Y162F mutant with aerobically reconstituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F6L
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase small subunit
- EC
- 1.17.4.1
- UniProt
- Q5KW80
- Ligands
- PLM, MN3, MN, FE
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase small subunit (EC 1.17.4.1) | protein | 284 | 81% helix, 0% strand | Q5KW80 |
| B | Ribonucleotide reductase small subunit (EC 1.17.4.1) | protein | 272 | 80% helix, 0% strand | Q5KW80 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- MN3 · Manganese (III) ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.84 | 0.97 | 38 | PLM |
| 2 | 221 | 0.78 | 0.91 | 41 | PLM |
| 3 | 100 | 0.73 | 0.95 | 21 | empty |
| 4 | 119 | 0.49 | 0.80 | 23 | empty |
| 5 | 117 | 0.43 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2712 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6F6L · R2-like ligand-binding oxidase Y162F mutant with aerobically reconstituted Mn/Fe cofactor · 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 Q5KW80
- Elsewhere: RCSB PDB 6F6L · PDBe 6F6L · UniProt Q5KW80
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