Research workbench
Crystal structure of human ubiquitous mitochondrial creatine kinase
Analyse Crystal structure of human ubiquitous mitochondrial creatine kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QK1
- Type
- protein
- Length
- 3,032 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creatine kinase, ubiquitous mitochondrial
- EC
- 2.7.3.2
- UniProt
- P12532
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Creatine kinase, ubiquitous mitochondrial (EC 2.7.3.2) | protein | 379 | 36% helix, 16% strand | P12532 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.84 | 0.85 | 89 | empty |
| 2 | 1097 | 0.84 | 0.85 | 86 | empty |
| 3 | 1102 | 0.83 | 0.85 | 91 | empty |
| 4 | 1075 | 0.83 | 0.84 | 88 | empty |
| 5 | 700 | 0.77 | 0.82 | 78 | empty |
Interfaces
24 interfaces between chains.
- A–E · 1107 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1102 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1092 Ų buried · 27 hydrogen bonds · protein-protein
- C–G · 1086 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 841 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1QK1 · Crystal structure of human ubiquitous mitochondrial creatine kinase · the same entry in another collection · chain H against H, TM-score 1.00
- P12532 · AlphaFold monomer V2.0 prediction for creatine kinase U-type, mitochondrial (P12532) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P12532
- Elsewhere: RCSB PDB 1QK1 · PDBe 1QK1 · UniProt P12532
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