MolNFT v1 · #165315 · protein
Crystal structure of ribonucleotide reductase nrdf L61G variant from bacillus anthracis aerobically soaked with FE(II) and MN(II) ions
6TQZ · Ribonucleoside-diphosphate reductase subunit beta: “Crystal structure of ribonucleotide reductase nrdf L61G variant from bacillus anthracis aerobically soaked…”. X-ray diffraction, 3 ligands (FE2, MN, SO4), 9 pockets (best…
- PDB
- 6TQZ
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- Q81TB4
- Ligands
- FE2, MN, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 285 | 78% helix, 0% strand | Q81TB4 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 287 | 78% helix, 0% strand | Q81TB4 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 18 | empty |
| 2 | 51 | 0.71 | 0.98 | 18 | empty |
| 3 | 225 | 0.51 | 0.75 | 29 | SO4 |
| 4 | 136 | 0.46 | 0.77 | 20 | SO4 |
| 5 | 68 | 0.43 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2368 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6TQZ · Crystal structure of ribonucleotide reductase NrdF L61G variant from Bacillus anthracis… · 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 Q81TB4
- Elsewhere: RCSB PDB 6TQZ · PDBe 6TQZ · UniProt Q81TB4
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