MolNFT v1 · #75747 · protein
The crystal structure of agmatine ureohydrolase of thermoplasma volcanium
3PZL: “The crystal structure of agmatine ureohydrolase of thermoplasma volcanium”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.77). MolNFT v1 #75747 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3PZL
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatine ureohydrolase
- UniProt
- Q97BB8
- Ligands
- MN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Agmatine ureohydrolase | protein | 290 | 42% helix, 21% strand | Q97BB8 |
| B | Agmatine ureohydrolase | protein | 293 | 41% helix, 20% strand | Q97BB8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.77 | 0.89 | 52 | empty |
| 2 | 738 | 0.69 | 0.76 | 60 | empty |
| 3 | 185 | 0.64 | 0.85 | 32 | empty |
| 4 | 199 | 0.64 | 0.84 | 35 | empty |
| 5 | 158 | 0.61 | 0.85 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1096 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1082 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1075 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3PZL · The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium · 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 Q97BB8
- Elsewhere: RCSB PDB 3PZL · PDBe 3PZL · UniProt Q97BB8
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