8P73: CAK

Cryo-EM structure of CAK in complex with inhibitor ICEC0829. Determined by electron microscopy at 2.0 Å resolution. Released 20 Mar 2024.

Method
Electron microscopy
Resolution
2.0 Å
Organism
Homo sapiens
Chains
3
Atoms
5,169
Mol. weight
88.14 kDa
Ligands
X58, X50
Released
20 Mar 2024

Explore 8P73 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P73 contains 43 α-helices and 11 β-strands across 3 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 H: 6 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix259-2624
α-helix263-2697
α-helix271-2744
α-helix276-2794
α-helix280-2856
α-helix289-30113
Chain I: 20 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-43
α-helix6-105
α-helix16-3621
α-helix48-492
α-helix50-7021
α-helix75-762
α-helix77-9216
α-helix101-11616
α-helix122-1265
α-helix133-15321
α-helix164-17714
α-helix184-1874
α-helix188-20013
α-helix203-2053
α-helix209-22315
α-helix229-2302
α-helix231-2355
α-helix243-26119
α-helix264-2663
α-helix267-28216
Chain J: 17 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand14-2071
β-strand25-2951
β-strand38-4141
α-helix57-6610
β-strand7412
β-strand77-8151
β-strand88-9251
β-strand96-9722
α-helix98-1036
α-helix111-13020
β-strand133-13423
α-helix140-1423
β-strand143-14532
β-strand151-15332
α-helix156-1583
β-strand160-16123
α-helix176-1783
α-helix181-1844
α-helix193-20816
α-helix218-22912
α-helix240-2423
α-helix257-2604
α-helix266-27510
α-helix284-2852
α-helix286-2905
α-helix293-2964
α-helix300-3034
α-helix304-3063

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CDK-activating kinase assembly factor MAT1Hprotein93Homo sapiensP51948 (AlphaFold model)
Cyclin-HIprotein324Homo sapiensP51946 (AlphaFold model)
Cyclin-dependent kinase 7Jprotein349Homo sapiensP50613 (AlphaFold model)
Sequence of entity 1 (H), FASTA
>8P73_1 CDK-activating kinase assembly factor MAT1 (chains H)
SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVR
AASPQDLAGGYTSSLACHRALQDAFSGLFWQPS
Sequence of entity 2 (I), FASTA
>8P73_2 Cyclin-H (chains I)
XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKY
YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN
VSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP
ILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLK
ENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYED
DDYVSKKSKHEEEEWTDDDLVESL
Sequence of entity 3 (J), FASTA
>8P73_3 Cyclin-dependent kinase 7 (chains J)
SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINR
TALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAY
MLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRW
YRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQW
PDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSN
RPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Ligands and cofactors

IDNameFormulaCopies
X58(3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-y…C22 H30 N6 O21
X50(3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-y…C22 H30 N6 O21

Primary citation

High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Cushing, V.I., Koh, A.F., Feng, J. et al. Nat Commun (2024) 15:2265-2265. DOI 10.1038/s41467-024-46375-9 · PubMed

Other PDB entries of the same protein (UniProt P51948 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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