Research workbench
Protein arginine kinase mcsb in the AMP-pn-bound state
Analyse Protein arginine kinase mcsb in the AMP-pn-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FH2
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine kinase
- EC
- 2.7.14.1
- UniProt
- P0DMM5
- Ligands
- AN2
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine kinase (EC 2.7.14.1) | protein | 353 | 49% helix, 16% strand | P0DMM5 |
| B | Protein-arginine kinase (EC 2.7.14.1) | protein | 304 | 55% helix, 15% strand | P0DMM5 |
Ligands and binding sites
- AN2 · Amp phosphoramidate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.82 | 0.89 | 57 | AN2, EDO |
| 2 | 299 | 0.69 | 0.84 | 46 | EDO |
| 3 | 97 | 0.50 | 0.82 | 17 | empty |
| 4 | 213 | 0.47 | 0.74 | 27 | empty |
| 5 | 94 | 0.37 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 15 hydrogen bonds · protein-protein
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 P0DMM5
- Elsewhere: RCSB PDB 6FH2 · PDBe 6FH2 · UniProt P0DMM5
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