MolNFT v1 · #105859 · protein
Crystal structure of T. brucei arginase-like protein quadruple mutant S149D/R151H/S153D/S226D
4RHM: “Crystal structure of T. brucei arginase-like protein quadruple mutant S149D/R151H/S153D/S226D”. X-ray diffraction, 1 ligand (MN), 17 pockets (best druggability 0.86). MolNFT v1 #105859 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RHM
- Type
- protein
- Length
- 916 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- Q581Y0
- Ligands
- MN
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 308 | 36% helix, 19% strand | Q581Y0 |
| B | Arginase (EC 3.5.3.1) | protein | 306 | 37% helix, 19% strand | Q581Y0 |
| C | Arginase (EC 3.5.3.1) | protein | 302 | 36% helix, 19% strand | Q581Y0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.86 | 0.97 | 39 | EDO |
| 2 | 73 | 0.55 | 0.87 | 19 | GOL |
| 3 | 81 | 0.55 | 0.86 | 26 | empty |
| 4 | 162 | 0.55 | 0.80 | 33 | empty |
| 5 | 72 | 0.52 | 0.85 | 17 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1239 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1237 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4RHM · Crystal structure of T. brucei arginase-like protein quadruple mutant… · 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 4RHM · PDBe 4RHM · UniProt Q581Y0
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