MolNFT v1 · #18472 · protein
Human arginase II: crystal structure and physiological role in male and female sexual arousal
1PQ3 · Arginase II, mitochondrial precursor: “Human arginase II: crystal structure and physiological role in male and female sexual arousal”. X-ray diffraction, 4 ligands (S2C, MN, SO4), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 1PQ3
- Type
- protein
- Length
- 1,836 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase II, mitochondrial precursor
- EC
- 3.5.3.1
- UniProt
- P78540
- Ligands
- S2C, MN, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Arginase II, mitochondrial precursor (EC 3.5.3.1) | protein | 306 | 42% helix, 17% strand | P78540 |
Ligands and binding sites
- S2C · S-2-(boronoethyl)-L-cysteine · ligand · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, F
- CL · Chloride ion · ion · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.81 | 0.82 | 76 | empty |
| 2 | 1076 | 0.79 | 0.81 | 70 | empty |
| 3 | 188 | 0.78 | 0.93 | 20 | empty |
| 4 | 217 | 0.56 | 0.79 | 35 | empty |
| 5 | 224 | 0.53 | 0.77 | 30 | empty |
Interfaces
9 interfaces between chains.
- D–E · 671 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 670 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 645 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 640 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1PQ3 · Human Arginase II: Crystal Structure and Physiological Role in Male and Female Sexual… · the same entry in another collection · chain F against F, TM-score 1.00
- P78540 · AlphaFold monomer V2.0 prediction for arginase-2, mitochondrial (P78540) · a predicted model of the same protein · chain D 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 P78540
- Elsewhere: RCSB PDB 1PQ3 · PDBe 1PQ3 · UniProt P78540
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.