Research workbench
Ribonucleotide reductase DIMANGANESE(II)-nrdf from escherichia COLI in complex with nrdi
Analyse Ribonucleotide reductase DIMANGANESE(II)-nrdf from escherichia COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N39
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 2 subunit beta; Protein nrdi
- EC
- 1.17.4.1
- UniProt
- P37146, P0A772
- Ligands
- FMN, MN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ribonucleoside-diphosphate reductase 2 subunit beta (EC 1.17.4.1) | protein | 282 | 80% helix, 0% strand | P37146 |
| C, D | Protein nrdi | protein | 128 | 39% helix, 20% strand | P0A772 |
| A | Ribonucleoside-diphosphate reductase 2 subunit beta (EC 1.17.4.1) | protein | 282 | 76% helix, 0% strand | P37146 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C, A, D
- MN · Manganese (II) ion · metal · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.74 | 0.86 | 41 | FMN |
| 2 | 303 | 0.73 | 0.86 | 43 | FMN |
| 3 | 200 | 0.52 | 0.77 | 27 | empty |
| 4 | 160 | 0.51 | 0.78 | 24 | empty |
| 5 | 140 | 0.41 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1716 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1108 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1036 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3N39 · Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with NrdI · the same entry in another collection · chain B against B, TM-score 1.00
- P37146 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 2 subunit beta… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0A772 · AlphaFold monomer V2.0 prediction for protein nrdi (P0A772) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P37146
- Every structure of UniProt P0A772
- Elsewhere: RCSB PDB 3N39 · PDBe 3N39 · UniProt P37146 · UniProt P0A772
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