MolNFT v1 · #105856 · protein
Crystal structure of wild-type T. brucei arginase-like protein in a reduced form
4RHJ: “Crystal structure of wild-type T. brucei arginase-like protein in a reduced form”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #105856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RHJ
- Type
- protein
- Length
- 1,727 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- Q581Y0
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 289 | 29% helix, 20% strand | Q581Y0 |
| B | Arginase (EC 3.5.3.1) | protein | 286 | 29% helix, 19% strand | Q581Y0 |
| C | Arginase (EC 3.5.3.1) | protein | 287 | 30% helix, 19% strand | Q581Y0 |
| D | Arginase (EC 3.5.3.1) | protein | 290 | 33% helix, 19% strand | Q581Y0 |
| E | Arginase (EC 3.5.3.1) | protein | 287 | 31% helix, 19% strand | Q581Y0 |
| F | Arginase (EC 3.5.3.1) | protein | 288 | 33% helix, 19% strand | Q581Y0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.72 | 0.78 | 87 | empty |
| 2 | 646 | 0.69 | 0.77 | 72 | empty |
| 3 | 309 | 0.68 | 0.83 | 45 | empty |
| 4 | 345 | 0.67 | 0.81 | 46 | EDO |
| 5 | 515 | 0.67 | 0.78 | 75 | empty |
Interfaces
8 interfaces between chains.
- A–E · 322 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 0 hydrogen bonds · protein-protein
- B–F · 187 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 166 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 153 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RHJ · Crystal structure of wild-type T. brucei arginase-like protein in a reduced form · 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 Q581Y0
- Elsewhere: RCSB PDB 4RHJ · PDBe 4RHJ · UniProt Q581Y0
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