MolNFT v1 · #177804 · protein
Crystal structure of N(OMEGA)-hydroxy-L-arginine hydrolase in complex with L-orn
7EUK · N(OMEGA)-hydroxy-L-arginine amidinohydrolase: “Crystal structure of N(OMEGA)-hydroxy-L-arginine hydrolase in complex with L-orn”. X-ray diffraction, 3 ligands (ORN, MN, MG), 5 pockets (best druggability 0.73). MolNFT v1 #177804 on…
- PDB
- 7EUK
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N(OMEGA)-hydroxy-L-arginine amidinohydrolase
- EC
- 3.5.3.25
- UniProt
- D2Z025
- Ligands
- ORN, MN, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N(OMEGA)-hydroxy-L-arginine amidinohydrolase (EC 3.5.3.25) | protein | 271 | 45% helix, 15% strand | D2Z025 |
| B | N(OMEGA)-hydroxy-L-arginine amidinohydrolase (EC 3.5.3.25) | protein | 273 | 46% helix, 15% strand | D2Z025 |
Ligands and binding sites
- ORN · L-ornithine · ligand · chains B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.73 | 0.85 | 35 | empty |
| 2 | 131 | 0.67 | 0.89 | 24 | empty |
| 3 | 200 | 0.65 | 0.85 | 39 | empty |
| 4 | 118 | 0.48 | 0.80 | 24 | ORN |
| 5 | 60 | 0.30 | 0.75 | 22 | MG |
Interfaces
1 interface between chains.
- A–B · 1249 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7EUK · Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with L-Orn · the same entry in another collection · chain A against A, TM-score 1.00
- D2Z025 · AlphaFold monomer V2.0 prediction for N(OMEGA)-hydroxy-L-arginine amidinohydrolase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 D2Z025
- Elsewhere: RCSB PDB 7EUK · PDBe 7EUK · UniProt D2Z025
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