Research workbench
Altering the binuclear manganese cluster of arginase diminishes thermostability and catalytic function
Analyse Altering the binuclear manganese cluster of arginase diminishes thermostability… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RLA
- Type
- protein
- Length
- 942 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.94
- Source
- Rattus norvegicus
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- P07824
- Ligands
- MN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.94 · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase (EC 3.5.3.1) | protein | 314 | 42% helix, 16% strand | P07824 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.80 | 0.82 | 70 | empty |
| 2 | 241 | 0.57 | 0.78 | 34 | empty |
| 3 | 254 | 0.56 | 0.78 | 33 | empty |
| 4 | 297 | 0.55 | 0.76 | 34 | empty |
| 5 | 106 | 0.48 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 955 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 954 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 930 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4RLA · Altering the binuclear manganese cluster of arginase diminishes thermostability and… · the same entry in another collection · chain A against A, TM-score 1.00
- P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · 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 P07824
- Elsewhere: RCSB PDB 4RLA · PDBe 4RLA · UniProt P07824
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