Research workbench
Substitution of manganese for iron in ribonucleotide reductase from escherichia COLI. spectroscopic and crystallographic characterization
Analyse Substitution of manganese for iron in ribonucleotide reductase from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MRR
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase R1 protein
- EC
- 1.17.4.1
- UniProt
- P69924
- Ligands
- HG, MN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleotide reductase R1 protein (EC 1.17.4.1) | protein | 340 | 71% helix, 4% strand | P69924 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 13 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.73 | 0.92 | 30 | empty |
| 2 | 59 | 0.54 | 0.88 | 17 | HG |
| 3 | 51 | 0.47 | 0.85 | 12 | empty |
| 4 | 50 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3098 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1MRR · Substitution of manganese for iron in ribonucleotide reductase from escherichia COLI.… · the same entry in another collection · chain A against A, TM-score 1.00
- P69924 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 1 subunit beta… · a predicted model of the same protein · chain A 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 P69924
- Elsewhere: RCSB PDB 1MRR · PDBe 1MRR · UniProt P69924
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