8R9U: 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 1.94 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,971
Mol. weight: 85.45 kDa
Ligands: YNK
Released: 29 May 2024

Explore 8R9U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R9U contains 31 α-helices and 24 β-strands across 2 chains. 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	1
β-strand	25-31	7	1
β-strand	37-42	6	1
α-helix	60-66	7
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	98-103	6
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	176-178	3
α-helix	181-184	4
α-helix	192-208	17
α-helix	218-229	12
α-helix	238-242	5
β-strand	248	1	4
α-helix	249-251	3
α-helix	257-260	4
α-helix	266-275	10
α-helix	286-290	5
α-helix	293-295	3
α-helix	300-303	4
α-helix	304-306	3

Chain B: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	5
β-strand	25-31	7	5
β-strand	37-40	4	5
α-helix	57-68	12
β-strand	74	1	6
β-strand	77-81	5	5
β-strand	88-92	5	5
β-strand	96-97	2	6
α-helix	98-103	6
α-helix	111-130	20
β-strand	133-134	2	7
α-helix	140-142	3
β-strand	143-145	3	6
β-strand	151-153	3	6
β-strand	160-161	2	7
α-helix	176-178	3
α-helix	181-184	4
α-helix	193-208	16
α-helix	218-229	12
α-helix	238-242	5
β-strand	248	1	4
α-helix	257-260	4
α-helix	266-275	10
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, B	protein	371	Homo sapiens	P50613 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8R9U_1 Cyclin-dependent kinase 7 (chains A, B)
MSYYHHHHHHDYDIPTTENLYFQGSMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTN
QIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFME
TDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHRILHRDLKPNNLLLDENGVLKLAD
FGLAKSFGDPNRAYEHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPG
DSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGL
FLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEAL
EQGGLPKKLIF

Ligands and cofactors

ID	Name	Formula	Copies
YNK	7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(triflu…	C23 H26 F3 N6 O P	2

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
8R9A 1.71 Å, A soakable crystal form of human CDK7 in complex with AMP-PNP
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

Browse structure collections

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