Research workbench
Crystal structure of dimeric arginine kinase in complex with amppnp and arginine
Analyse Crystal structure of dimeric arginine kinase in complex with amppnp and arginine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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