MolNFT v1 · #68380 · protein
Crystal structure of dimeric arginine kinase in complex with amppnp and arginine
3JU6: “Crystal structure of dimeric arginine kinase in complex with amppnp and arginine”. X-ray diffraction, 2 ligands (ARG, ANP), 11 pockets (best druggability 0.81). MolNFT v1 #68380 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3JU6
- Type
- protein
- Length
- 1,446 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
- ARG, ANP
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine kinase (EC 2.7.3.3) | protein | 361 | 39% helix, 16% strand | Q9XY07 |
| B | Arginine kinase (EC 2.7.3.3) | protein | 362 | 38% helix, 16% strand | Q9XY07 |
| C | Arginine kinase (EC 2.7.3.3) | protein | 363 | 38% helix, 16% strand | Q9XY07 |
| D | Arginine kinase (EC 2.7.3.3) | protein | 360 | 38% helix, 16% strand | Q9XY07 |
Ligands and binding sites
- ARG · Arginine · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.81 | 0.87 | 80 | empty |
| 2 | 655 | 0.80 | 0.85 | 83 | empty |
| 3 | 546 | 0.71 | 0.80 | 56 | empty |
| 4 | 521 | 0.64 | 0.76 | 56 | ARG, ANP |
| 5 | 391 | 0.56 | 0.74 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1569 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1521 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 144 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 3JU6 · Crystal Structure of Dimeric Arginine Kinase in Complex with AMPPNP and Arginine · the same entry in another collection · chain C against C, TM-score 1.00
- Q9XY07 · AlphaFold monomer V2.0 prediction for arginine kinase (Q9XY07) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 3JU6 · PDBe 3JU6 · UniProt Q9XY07
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