6GZH: Human CDK9/cyclinT1 with A86

Crystal Structure of Human CDK9/cyclinT1 with A86. Determined by X-ray diffraction at 3.17 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 3.17 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,763
Mol. weight: 118.86 kDa
Ligands: LCI
Released: 29 Aug 2018

Explore 6GZH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GZH contains 30 α-helices and 16 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-26	8	1
β-strand	33-38	6	1
β-strand	44-49	6	1
α-helix	61-72	12
β-strand	75	1	2
β-strand	78	1	2
α-helix	79-80	2
β-strand	81-86	6	1
β-strand	99-104	6	1
β-strand	108-109	2	2
α-helix	110-114	5
α-helix	123-142	20
β-strand	145-146	2	3
β-strand	155-157	3	2
β-strand	163-165	3	2
β-strand	172-173	2	3
α-helix	192-194	3
α-helix	197-200	4
α-helix	209-224	16
α-helix	234-245	12
α-helix	256-258	3
α-helix	261-264	4
β-strand	273	1	4
α-helix	275-279	5
α-helix	286-295	10
α-helix	306-310	5
α-helix	320-321	2

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
α-helix	23-27	5
α-helix	33-52	20
α-helix	56-69	14
α-helix	80-94	15
α-helix	101-112	12
α-helix	117-120	4
α-helix	124-144	21
α-helix	154-161	8
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-208	16
β-strand	215	1	5
β-strand	219	1	5
α-helix	221-224	4
α-helix	231-247	17
α-helix	251-254	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 9	A	protein	326	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B	protein	726	Homo sapiens	O60563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GZH_1 Cyclin-dependent kinase 9 (chains A)
MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFP
ITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVK
FTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNS
QPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLAL
ISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDP
AQRIDSDDALNHDFFWSDPMPSDLKG

Sequence of entity 2 (B), FASTA

>6GZH_2 Cyclin-T1 (chains B)
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTIN
TAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLPD
TRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATN
SLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHE
LLQILEKTPNRLKRIWNWRACEAAKKTKADDRGTDEKTSEQTILNMISQSSSDTTIAGLM
SMSTSTTSAVPSLPVSEESSSNLTSVEMLPGKRWLSSQPSFKLEPTQGHRTSENLALTGV
DHSLPQDGSNAFISQKQNSKSVPSAKVSLKEYRAKHAEELAAQKRQLENMEANVKSQYAY
AAQNLLSHHDSHSSVILKMPIEGSENPERPFLEKADKTALKMRIPVAGGDKAASSKPEEI
KMRIKVHAAADKHNSVEDSVTKSREHKEKHKTHPSNHHHHHNHHSHKHSHSQLPVGTGNK
RPGDPKHSSQTSNLAHKTYSLSSSFSSSSSTRKRGPSEETGGAVFDHPAKIAKSTKSSSL
NFSFPSLPTMGQMPGHSSDTSGLSFSQPSCKTRVPHSKLDKGPTGANGHNTTQTIDYQDT
VNMLHSLLSAQGVQPTQPTAFEFVRPYSDYLNPRSGGISSRSGNTDKPRPPPLPSEPPPP
LPPLPK

Ligands and cofactors

ID	Name	Formula	Copies
LCI	[4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl…	C18 H26 F N6	1

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

Primary citation

Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models. Minzel, W., Venkatachalam, A., Fink, A. et al. Cell (2018) 175:171-185.e25. DOI 10.1016/j.cell.2018.07.045 · PubMed

Other PDB entries of the same protein (UniProt P50750 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MI9 2.1 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb
3BLH 2.48 Å, Crystal Structure of Human CDK9/cyclinT1
3BLR 2.8 Å, Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol
3MY1 2.8 Å, Structure of CDK9/cyclinT1 in complex with DRB
7NWK 2.81 Å, Crystal structure of CDK9-Cyclin T1 bound by compound 6
3BLQ 2.9 Å, Crystal Structure of Human CDK9/cyclinT1 in Complex with ATP
4OR5 2.9 Å, Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4
4IMY 2.94 Å, The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat
3TN8 2.95 Å, CDK9/cyclin T in complex with CAN508
4BCH 2.96 Å, Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine…
3LQ5 3.0 Å, Structure of CDK9/CyclinT in complex with S-CR8
3MIA 3.0 Å, Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb

Browse structure collections

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