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X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde alpha subunit with ttp, ATP, and ADP
Analyse X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MT9
- Type
- protein
- Length
- 679 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
- TTP, ADP, ATP, MG
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 679 | 48% helix, 12% strand | A0A162Q3J9 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.57 | 0.77 | 42 | empty |
| 2 | 56 | 0.51 | 0.87 | 15 | empty |
| 3 | 178 | 0.46 | 0.75 | 27 | empty |
| 4 | 121 | 0.45 | 0.78 | 24 | empty |
| 5 | 101 | 0.40 | 0.76 | 14 | TTP |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6MT9 · 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 6MT9 · PDBe 6MT9 · UniProt A0A162Q3J9
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