Research workbench
The structure of agmatinase from E. COLI at 3.2 a displaying guanidine in the active site
Analyse The structure of agmatinase from E. COLI at 3.2 a displaying guanidine in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOX
- Type
- protein
- Length
- 852 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agmatinase
- EC
- 3.5.3.11
- UniProt
- A0A4S5B4F2
- Ligands
- GAI, MN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agmatinase (EC 3.5.3.11) | protein | 284 | 41% helix, 18% strand | A0A4S5B4F2 |
| B | Agmatinase (EC 3.5.3.11) | protein | 283 | 40% helix, 17% strand | A0A4S5B4F2 |
| C | Agmatinase (EC 3.5.3.11) | protein | 285 | 41% helix, 18% strand | A0A4S5B4F2 |
Ligands and binding sites
- GAI · Guanidine · ligand · 4 copies · chains A, C, B
- 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.71 | 0.82 | 41 | empty |
| 2 | 190 | 0.54 | 0.79 | 31 | GAI |
| 3 | 180 | 0.50 | 0.77 | 30 | GAI |
| 4 | 176 | 0.48 | 0.76 | 30 | GAI |
Interfaces
3 interfaces between chains.
- A–B · 959 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 917 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 880 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7LOX · The structure of Agmatinase from E. Coli at 3.2 A displaying guanidine in the active site · 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 A0A4S5B4F2
- Elsewhere: RCSB PDB 7LOX · PDBe 7LOX · UniProt A0A4S5B4F2
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