MolNFT v1 · #145186 · protein
X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde alpha subunit damp-bound (pH 7)
6CGN · Ribonucleoside-diphosphate reductase: “X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde alpha subunit damp-bound (pH 7)”. X-ray diffraction, 2 ligands (DA, PO4), 10 pockets (best druggability 0.68). MolNFT…
- PDB
- 6CGN
- Type
- protein
- Length
- 674 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- A0A162Q3J9
- Ligands
- DA, PO4
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 674 | 47% helix, 13% strand | A0A162Q3J9 |
Ligands and binding sites
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.68 | 0.80 | 55 | empty |
| 2 | 91 | 0.58 | 0.86 | 18 | empty |
| 3 | 88 | 0.51 | 0.83 | 20 | empty |
| 4 | 170 | 0.49 | 0.77 | 25 | empty |
| 5 | 131 | 0.46 | 0.77 | 20 | empty |
Compared structures
- 6CGN · X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit… · 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 A0A162Q3J9
- Elsewhere: RCSB PDB 6CGN · PDBe 6CGN · UniProt A0A162Q3J9
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