Research workbench
Crystal structure of human sarcomeric mitochondrial creatine kinase
Analyse Crystal structure of human sarcomeric 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
- 4Z9M
- Type
- protein
- Length
- 2,818 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creatine kinase S-type, mitochondrial
- EC
- 2.7.3.2
- UniProt
- P17540
- Ligands
- ADP, UNX
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 352 | 37% helix, 18% strand | P17540 |
| B | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 300 | 37% helix, 15% strand | P17540 |
| C, D | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 375 | 37% helix, 17% strand | P17540 |
| E | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 369 | 37% helix, 18% strand | P17540 |
| F | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 369 | 37% helix, 17% strand | P17540 |
| G | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 313 | 35% helix, 15% strand | P17540 |
| H | Creatine kinase S-type, mitochondrial (EC 2.7.3.2) | protein | 365 | 36% helix, 17% strand | P17540 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- UNX · Unknown atom or ion · ion · 71 copies · chains A, B, E, C, H, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.83 | 0.89 | 65 | ADP, UNX |
| 2 | 523 | 0.82 | 0.89 | 64 | ADP, UNX |
| 3 | 476 | 0.82 | 0.90 | 61 | ADP, UNX |
| 4 | 546 | 0.82 | 0.88 | 60 | ADP, UNX |
| 5 | 782 | 0.81 | 0.84 | 77 | UNX |
Interfaces
20 interfaces between chains.
- B–E · 1031 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1001 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 972 Ų buried · 22 hydrogen bonds · protein-protein
- C–H · 972 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 383 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4Z9M · Crystal structure of human sarcomeric mitochondrial creatine kinase · the same entry in another collection · chain H against H, TM-score 1.00
- P17540 · AlphaFold monomer V2.0 prediction for creatine kinase S-type, mitochondrial (P17540) · a predicted model of the same protein · chain B 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 P17540
- Elsewhere: RCSB PDB 4Z9M · PDBe 4Z9M · UniProt P17540
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.