Research workbench
Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily
Analyse Crystal structure of agmatinase reveals structural conservation and inhibition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WOG
- 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
- 16D, MN
- Pockets
- 17 · best druggability 0.86
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
- 16D · Hexane-1,6-diamine · ligand · 6 copies · chains A, B, C, D, E, F
- 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
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.86 | 0.87 | 89 | empty |
| 2 | 624 | 0.82 | 0.87 | 49 | empty |
| 3 | 454 | 0.76 | 0.84 | 51 | 16D |
| 4 | 468 | 0.75 | 0.84 | 46 | 16D |
| 5 | 486 | 0.75 | 0.84 | 48 | 16D |
Interfaces
12 interfaces between chains.
- A–E · 1197 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1195 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1191 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1164 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1158 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1WOG · 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 1WOG · PDBe 1WOG · UniProt Q9RZ04
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