Research workbench
Crystal structure of arginase from zymomonas mobilis ZM4
Analyse Crystal structure of arginase from zymomonas mobilis ZM4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KSY
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARGINASE/AGMATINASE/FORMIMINOGLUTAMASE
- UniProt
- Q5NQE9
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ARGINASE/AGMATINASE/FORMIMINOGLUTAMASE | protein | 286 | 41% helix, 17% strand | Q5NQE9 |
| B | ARGINASE/AGMATINASE/FORMIMINOGLUTAMASE | protein | 289 | 41% helix, 16% strand | Q5NQE9 |
| C | ARGINASE/AGMATINASE/FORMIMINOGLUTAMASE | protein | 284 | 42% helix, 16% strand | Q5NQE9 |
| D | ARGINASE/AGMATINASE/FORMIMINOGLUTAMASE | protein | 286 | 41% helix, 17% strand | Q5NQE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.69 | 0.79 | 65 | empty |
| 2 | 546 | 0.69 | 0.79 | 59 | empty |
| 3 | 149 | 0.58 | 0.83 | 22 | empty |
| 4 | 143 | 0.56 | 0.82 | 22 | empty |
| 5 | 156 | 0.55 | 0.80 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2165 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KSY · Crystal structure of arginase from Zymomonas mobilis ZM4 · 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 Q5NQE9
- Elsewhere: RCSB PDB 6KSY · PDBe 6KSY · UniProt Q5NQE9
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