MolNFT v1 · #169439 · protein
Structure of the human cdk-activating kinase
6XBZ · Cdk-activating kinase assembly factor MAT1: “Structure of the human cdk-activating kinase”. Electron microscopy, 2 ligands (AGS, MG), 9 pockets (best druggability 0.76). MolNFT v1 #169439 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XBZ
- Type
- protein
- Length
- 644 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdk-activating kinase assembly factor MAT1; Cyclin-H; Cyclin-dependent kinase 7
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P51948, P51946, P50613
- Ligands
- AGS, MG
- Pockets
- 9 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Cdk-activating kinase assembly factor MAT1 | protein | 65 | 35% helix, 3% strand | P51948 |
| I | Cyclin-H | protein | 281 | 69% helix, 0% strand | P51946 |
| J | Cyclin-dependent kinase 7 (EC 2.7.11.22, 2.7.11.23) | protein | 298 | 34% helix, 18% strand | P50613 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains J
- MG · Magnesium ion · metal · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.76 | 0.86 | 63 | empty |
| 2 | 488 | 0.69 | 0.79 | 42 | empty |
| 3 | 296 | 0.61 | 0.79 | 34 | MG, AGS |
| 4 | 122 | 0.45 | 0.77 | 17 | empty |
| 5 | 62 | 0.38 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–J · 1256 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1232 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1180 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6XBZ · Structure of the human CDK-activating kinase · the same entry in another collection · chain H against H, TM-score 1.00
- P51946 · AlphaFold monomer V2.0 prediction for cyclin-H (P51946) · a predicted model of the same protein · chain I against A, TM-score 0.99
- P50613 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 7 (P50613) · a predicted model of the same protein · chain J against A, TM-score 0.92
- P51948 · AlphaFold monomer V2.0 prediction for cdk-activating kinase assembly factor MAT1 (P51948) · a predicted model of the same protein · chain H against A, TM-score 0.78
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 P51948
- Every structure of UniProt P51946
- Every structure of UniProt P50613
- Elsewhere: RCSB PDB 6XBZ · PDBe 6XBZ · UniProt P51948 · UniProt P51946 · UniProt P50613
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