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The 2.1 structure of T. californica creatine kinase complexed with the transition-state analogue complex, ADP- mg 2+ /NO3-/creatine
Analyse The 2.1 structure of T. californica creatine kinase complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VRP
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creatine kinase, M chain
- EC
- 2.7.3.2
- UniProt
- P04414
- Ligands
- ADP, IOM, MG, NO3
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creatine kinase, M chain (EC 2.7.3.2) | protein | 370 | 38% helix, 16% strand | P04414 |
| B | Creatine kinase, M chain (EC 2.7.3.2) | protein | 374 | 38% helix, 16% strand | P04414 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- IOM · (diaminomethyl-methyl-amino)-acetic acid · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.82 | 0.90 | 62 | MG, NO3, ADP, IOM |
| 2 | 1035 | 0.79 | 0.81 | 83 | empty |
| 3 | 612 | 0.69 | 0.78 | 66 | MG, ADP |
| 4 | 150 | 0.44 | 0.76 | 25 | empty |
| 5 | 128 | 0.44 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1081 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1VRP · The 2.1 Structure of T. californica Creatine Kinase Complexed with the Transition-State… · the same entry in another collection · chain A against A, TM-score 1.00
- P04414 · AlphaFold monomer V2.0 prediction for creatine kinase M-type (P04414) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P04414
- Elsewhere: RCSB PDB 1VRP · PDBe 1VRP · UniProt P04414
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