Research workbench
X-ray structure of rat arginase I-T135A: the unliganded complex
Analyse X-ray structure of rat arginase I-T135A: the unliganded complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8Q
- Type
- protein
- Length
- 924 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1
- EC
- 3.5.3.1
- UniProt
- P07824
- Ligands
- MN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase-1 (EC 3.5.3.1) | protein | 308 | 40% helix, 16% strand | P07824 |
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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.81 | 0.85 | 51 | empty |
| 2 | 345 | 0.57 | 0.75 | 41 | empty |
| 3 | 301 | 0.56 | 0.76 | 32 | empty |
| 4 | 188 | 0.54 | 0.79 | 28 | empty |
| 5 | 135 | 0.52 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 762 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 755 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 740 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 P07824
- Elsewhere: RCSB PDB 3E8Q · PDBe 3E8Q · UniProt P07824
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