MolNFT v1 · #141640 · protein
Crystal structure of entamoeba histolytica arginase in complex with N(OMEGA)-hydroxy-L-arginine (noha) at 1.74 a
5ZEE: “Crystal structure of entamoeba histolytica arginase in complex with N(OMEGA)-hydroxy-L-arginine (noha) at…”. X-ray diffraction, 2 ligands (HAR, MN), 5 pockets (best druggability 0.47). MolNFT v1 #141640 on GenesisL1: 3D structure…
- PDB
- 5ZEE
- Type
- protein
- Length
- 592 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
- HAR, MN
- Pockets
- 5 · best druggability 0.47
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 | 295 | 40% helix, 17% strand | C4LSS0 |
| B | Arginase (EC 3.5.3.1) | protein | 297 | 40% helix, 16% strand | C4LSS0 |
Ligands and binding sites
- HAR · N-omega-hydroxy-L-arginine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · 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 | 116 | 0.47 | 0.79 | 21 | empty |
| 2 | 77 | 0.41 | 0.80 | 20 | HAR |
| 3 | 83 | 0.41 | 0.79 | 20 | HAR |
| 4 | 85 | 0.38 | 0.77 | 18 | empty |
| 5 | 64 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZEE · Crystal structure of Entamoeba histolytica Arginase in complex with… · the same entry in another collection · chain B against B, 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 5ZEE · PDBe 5ZEE · UniProt C4LSS0
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