MolNFT v1 · #26422 · protein
Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily
1WOI: “Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase…”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.82). MolNFT v1 #26422 on GenesisL1: 3D structure…
- PDB
- 1WOI
- Type
- protein
- Length
- 1,818 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatinase
- EC
- 3.5.3.11
- UniProt
- Q9RZ04
- Ligands
- MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Agmatinase (EC 3.5.3.11) | protein | 303 | 36% helix, 22% strand | Q9RZ04 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.82 | 0.87 | 47 | empty |
| 2 | 587 | 0.81 | 0.87 | 44 | empty |
| 3 | 571 | 0.81 | 0.87 | 47 | empty |
| 4 | 468 | 0.76 | 0.85 | 54 | empty |
| 5 | 454 | 0.75 | 0.84 | 46 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1196 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1186 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1185 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1165 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1164 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1WOI · Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism… · 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 Q9RZ04
- Elsewhere: RCSB PDB 1WOI · PDBe 1WOI · UniProt Q9RZ04
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