Research workbench
Crystal structure of the class I ribonucleotide reductase from pseudomonas aeruginosa in complex with datp
Analyse Crystal structure of the class I ribonucleotide reductase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IM3
- Type
- protein
- Length
- 1,734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- Q9I4I1
- Ligands
- DTP, MG
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 874 | 50% helix, 11% strand | Q9I4I1 |
| B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 860 | 51% helix, 13% strand | Q9I4I1 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.74 | 0.81 | 55 | empty |
| 2 | 565 | 0.73 | 0.81 | 66 | empty |
| 3 | 661 | 0.70 | 0.78 | 63 | empty |
| 4 | 483 | 0.67 | 0.78 | 59 | empty |
| 5 | 539 | 0.67 | 0.77 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5IM3 · Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in… · 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 Q9I4I1
- Elsewhere: RCSB PDB 5IM3 · PDBe 5IM3 · UniProt Q9I4I1
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