8P6Y: CAK

Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS. Determined by electron microscopy at 1.9 Å resolution. Released 30 Aug 2023.

Method
Electron microscopy
Resolution
1.9 Å
Organism
Homo sapiens
Chains
3
Atoms
5,266
Mol. weight
87.87 kDa
Ligands
MG, AGS
Released
30 Aug 2023

Explore 8P6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P6Y contains 45 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: 7 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix258-2625
α-helix263-2653
α-helix266-2694
α-helix271-2744
α-helix276-2794
α-helix280-2845
α-helix289-30113
Chain I: 20 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-43
α-helix6-105
α-helix16-3722
α-helix48-492
α-helix50-6920
α-helix74-763
α-helix77-9216
α-helix101-11515
α-helix122-1276
α-helix133-15321
α-helix164-17714
α-helix184-1874
α-helix188-19912
α-helix203-2053
α-helix209-22315
α-helix229-2302
α-helix231-2355
α-helix238-2403
α-helix242-26019
α-helix267-28317
Chain J: 18 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand14-1961
β-strand26-2941
β-strand38-4141
α-helix57-6610
β-strand7412
β-strand77-8371
β-strand86-9271
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-helix231-2333
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
>8P6Y_1 CDK-activating kinase assembly factor MAT1 (chains H)
SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVR
AASPQDLAGGYTSSLACHRALQDAFSGLFWQPS
Sequence of entity 2 (I), FASTA
>8P6Y_2 Cyclin-H (chains I)
XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKY
YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN
VSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP
ILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLK
ENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYED
DDYVSKKSKHEEEEWTDDDLVESL
Sequence of entity 3 (J), FASTA
>8P6Y_3 Cyclin-dependent kinase 7 (chains J)
SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINR
TALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAY
MLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRW
YRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQW
PDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSN
RPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S1

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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