MolNFT v1 · #50237 · protein
Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from bacillus halodurans at 1.90 a resolution
2RCC · Ribonucleoside-diphosphate reductase subunit beta: “Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from bacillus halodurans at 1.90…”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability…
- PDB
- 2RCC
- Type
- protein
- Length
- 904 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- Q9KFH7
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 313 | 66% helix, 1% strand | Q9KFH7 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 280 | 80% helix, 0% strand | Q9KFH7 |
| C | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 311 | 70% helix, 0% strand | Q9KFH7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.80 | 0.84 | 53 | GOL |
| 2 | 514 | 0.67 | 0.78 | 53 | empty |
| 3 | 68 | 0.64 | 0.92 | 17 | empty |
| 4 | 58 | 0.55 | 0.89 | 16 | empty |
| 5 | 89 | 0.41 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1746 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 509 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 modified (engineered).
Compared structures
- 2RCC · Crystal structure of putative class I ribonucleotide reductase (NP_241368.1) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KFH7 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit beta… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9KFH7
- Elsewhere: RCSB PDB 2RCC · PDBe 2RCC · UniProt Q9KFH7
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