MolNFT v1 · #141641 · protein
Crystal structure of entamoeba histolytica arginase in complex with L- norvaline at 2.01 a
5ZEF: “Crystal structure of entamoeba histolytica arginase in complex with L- norvaline at 2.01 a”. X-ray diffraction, 2 ligands (NVA, MN), 4 pockets (best druggability 0.48). MolNFT v1 #141641 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZEF
- Type
- protein
- Length
- 591 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
- NVA, MN
- Pockets
- 4 · best druggability 0.48
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 | 297 | 39% helix, 17% strand | C4LSS0 |
Ligands and binding sites
- NVA · Norvaline · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.48 | 0.81 | 24 | NVA |
| 2 | 88 | 0.43 | 0.80 | 19 | NVA |
| 3 | 97 | 0.39 | 0.77 | 18 | empty |
| 4 | 102 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZEF · Crystal structure of Entamoeba histolytica Arginase in complex with L- Norvaline at 2.01 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 5ZEF · PDBe 5ZEF · UniProt C4LSS0
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