Research workbench
Cryo-EM structure of the human cak bound to ICEC0942 (phenix-OPLS3E)
Analyse Cryo-EM structure of the human cak bound to ICEC0942 (phenix-OPLS3E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B5Q
- Type
- protein
- Length
- 643 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
- I74
- Pockets
- 6 · best druggability 0.75
Structure
electron microscopy · 3 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Cdk-activating kinase assembly factor MAT1 | protein | 65 | 32% helix, 0% strand | P51948 |
| I | Cyclin-H | protein | 281 | 70% helix, 0% strand | P51946 |
| J | Cyclin-dependent kinase 7 (EC 2.7.11.22, 2.7.11.23) | protein | 297 | 35% helix, 18% strand | P50613 |
Ligands and binding sites
- I74 · (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol · ligand · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.75 | 0.84 | 54 | empty |
| 2 | 428 | 0.69 | 0.81 | 43 | empty |
| 3 | 311 | 0.65 | 0.80 | 34 | I74 |
| 4 | 133 | 0.51 | 0.80 | 23 | empty |
| 5 | 62 | 0.40 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–I · 1260 Ų buried · 14 hydrogen bonds · protein-protein
- H–J · 1243 Ų buried · 6 hydrogen bonds · protein-protein
- I–J · 1097 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7B5Q · Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) · the same entry in another collection · chain I against I, 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 0.93
- 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 7B5Q · PDBe 7B5Q · UniProt P51948 · UniProt P51946 · UniProt P50613
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