8R9A: A soakable crystal form of human CDK7

A soakable crystal form of human CDK7 in complex with AMP-PNP. Determined by X-ray diffraction at 1.71 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 1.71 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,560
Mol. weight: 42.74 kDa
Ligands: I74
Released: 29 May 2024

Explore 8R9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R9A contains 19 α-helices and 11 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	1
β-strand	25-31	7	1
β-strand	37-41	5	1
α-helix	57-68	12
β-strand	74	1	2
β-strand	77-81	5	1
β-strand	88-92	5	1
β-strand	96-97	2	2
α-helix	98-102	5
α-helix	111-130	20
β-strand	133-134	2	3
α-helix	140-142	3
β-strand	143-145	3	2
β-strand	151-153	3	2
β-strand	160-161	2	3
α-helix	165-167	3
α-helix	176-178	3
α-helix	181-184	4
α-helix	193-208	16
α-helix	218-229	12
α-helix	231-233	3
α-helix	240-242	3
α-helix	249-251	3
α-helix	257-260	4
α-helix	266-275	10
α-helix	284-285	2
α-helix	286-290	5
α-helix	293-296	4
α-helix	300-303	4
α-helix	304-306	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 7	A	protein	371	Homo sapiens	P50613 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8R9A_1 Cyclin-dependent kinase 7 (chains A)
MSYYHHHHHHDYDIPTTENLYFQGSMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTN
QIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFME
TDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHRILHRDLKPNNLLLDENGVLKLAD
FGLAKSFGDPNRAYEHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPG
DSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGL
FLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEAL
EQGGLPKKLIF

Ligands and cofactors

ID	Name	Formula	Copies
I74	(3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-y…	C22 H30 N6 O	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design. Mukherjee, M., Day, P.J., Laverty, D. et al. Structure (2024) 32:1040-1048.e3. DOI 10.1016/j.str.2024.05.011 · PubMed

Other PDB entries of the same protein (UniProt P50613 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P79 1.7 Å, Cryo-EM structure of CAK with averaged inhibitor density
8P77 1.8 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0943
8R99 1.81 Å, A soakable crystal form of human CDK7 in complex with AMP-PNP
8ORM 1.9 Å, Cryo-EM structure of CAK-THZ1
8P6V 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0942
8P6W 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor BS-181
8P6X 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor BS-194
8P6Y 1.9 Å, Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS
8P72 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0768
8P78 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor dinaciclib
8PLZ 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor CT7030
8R9U 1.94 Å, A soakable crystal form of human CDK7 in complex with AMP-PNP

Browse structure collections

About this viewer

MolViewer shows 8R9A directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.