MolNFT v1 · #9251 · protein
Crystal structure of the H141C arginase variant complexed with products ornithine and urea
1HQG · Arginase 1: “Crystal structure of the H141C arginase variant complexed with products ornithine and urea”. X-ray diffraction, 3 ligands (ORN, URE, MN), 10 pockets (best druggability 0.81). MolNFT v1 #9251 on GenesisL1: 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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