MolNFT v1 · #147395 · protein
Crystal structure of the class ie ribonucleotide reductase beta subunit from aerococcus urinae in activated form
6EBP · Ribonucleoside-diphosphate reductase, beta subunit: “Crystal structure of the class ie ribonucleotide reductase beta subunit from aerococcus urinae in activated…”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability…
- PDB
- 6EBP
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase, beta subunit
- EC
- 1.17.4.1
- UniProt
- F2I8X9
- Ligands
- CA
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 303 | 77% helix, 1% strand | F2I8X9 |
| B, D | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 311 | 76% helix, 1% strand | F2I8X9 |
| C | Ribonucleoside-diphosphate reductase, beta subunit (EC 1.17.4.1) | protein | 304 | 76% helix, 1% strand | F2I8X9 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.56 | 0.82 | 31 | empty |
| 2 | 337 | 0.56 | 0.75 | 50 | GOL |
| 3 | 169 | 0.56 | 0.80 | 35 | empty |
| 4 | 296 | 0.48 | 0.72 | 34 | empty |
| 5 | 157 | 0.48 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2739 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 175 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6EBP · Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus… · 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 F2I8X9
- Elsewhere: RCSB PDB 6EBP · PDBe 6EBP · UniProt F2I8X9
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