MolNFT v1 · #68379 · protein
Crystal structure of dimeric arginine kinase at 1.75-a resolution
3JU5: “Crystal structure of dimeric arginine kinase at 1.75-a resolution”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.81). MolNFT v1 #68379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3JU5
- Type
- protein
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine kinase
- EC
- 2.7.3.3
- UniProt
- Q9XY07
- Ligands
- MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine kinase (EC 2.7.3.3) | protein | 363 | 39% helix, 17% strand | Q9XY07 |
| B | Arginine kinase (EC 2.7.3.3) | protein | 365 | 38% helix, 16% strand | Q9XY07 |
| C | Arginine kinase (EC 2.7.3.3) | protein | 367 | 39% helix, 16% strand | Q9XY07 |
| D | Arginine kinase (EC 2.7.3.3) | protein | 360 | 39% helix, 17% strand | Q9XY07 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.81 | 0.84 | 97 | MG |
| 2 | 609 | 0.79 | 0.85 | 75 | MG |
| 3 | 519 | 0.70 | 0.80 | 54 | empty |
| 4 | 437 | 0.60 | 0.75 | 53 | empty |
| 5 | 179 | 0.57 | 0.81 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1498 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1498 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
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 Q9XY07
- Elsewhere: RCSB PDB 3JU5 · PDBe 3JU5 · UniProt Q9XY07
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