Research workbench
Crystal structure of the H141C arginase variant complexed with products ornithine and urea
Analyse Crystal structure of the H141C arginase variant complexed with products… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HQG
- Type
- protein
- Length
- 942 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
- ORN, URE, MN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase 1 (EC 3.5.3.1) | protein | 314 | 41% helix, 16% strand | P07824 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 3 copies · chains A, B, C
- URE · Urea · ligand · 3 copies · chains A, B, C
- 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.81 | 0.83 | 78 | empty |
| 2 | 242 | 0.55 | 0.78 | 31 | empty |
| 3 | 220 | 0.55 | 0.78 | 28 | empty |
| 4 | 186 | 0.52 | 0.78 | 27 | empty |
| 5 | 67 | 0.46 | 0.83 | 21 | ORN, URE |
Interfaces
3 interfaces between chains.
- B–C · 985 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 969 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 946 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (artifact).
Compared structures
- 1HQG · Crystal structure of the H141C arginase variant complexed with products ornithine and urea · the same entry in another collection · chain B against B, TM-score 1.00
- P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · chain B 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 P07824
- Elsewhere: RCSB PDB 1HQG · PDBe 1HQG · UniProt P07824
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