MolNFT v1 · #141643 · protein
Crystal structure of entamoeba histolytica arginase in complex with L- ornithine at 2.35 a
5ZEH: “Crystal structure of entamoeba histolytica arginase in complex with L- ornithine at 2.35 a”. X-ray diffraction, 2 ligands (ORN, MN), 5 pockets (best druggability 0.42). MolNFT v1 #141643 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZEH
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase
- EC
- 3.5.3.1
- UniProt
- C4LSS0
- Ligands
- ORN, MN
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginase (EC 3.5.3.1) | protein | 294 | 40% helix, 17% strand | C4LSS0 |
| B | Arginase (EC 3.5.3.1) | protein | 293 | 40% helix, 17% strand | C4LSS0 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.42 | 0.80 | 18 | ORN, MN |
| 2 | 76 | 0.42 | 0.80 | 20 | ORN |
| 3 | 72 | 0.40 | 0.78 | 19 | empty |
| 4 | 85 | 0.39 | 0.77 | 19 | empty |
| 5 | 80 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5ZEH · Crystal structure of Entamoeba histolytica Arginase in complex with L- Ornithine at 2.35 A · 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 C4LSS0
- Elsewhere: RCSB PDB 5ZEH · PDBe 5ZEH · UniProt C4LSS0
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