3MY1: CDK9/cyclinT1

Structure of CDK9/cyclinT1 in complex with DRB. Determined by X-ray diffraction at 2.8 Å resolution. Released 29 Sept 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,699
Mol. weight: 69.05 kDa
Ligands: PO4, RFZ
Released: 29 Sept 2010

Explore 3MY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MY1 contains 32 α-helices and 13 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: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-24	6	2
β-strand	33-38	6	2
β-strand	44-49	6	2
α-helix	61-72	12
β-strand	78	1	3
β-strand	81-85	5	2
β-strand	86	1	1
β-strand	100-104	5	2
β-strand	108-109	2	3
α-helix	110-115	6
α-helix	123-142	20
β-strand	145-146	2	4
α-helix	152-154	3
β-strand	155-157	3	3
β-strand	163-165	3	3
β-strand	172-173	2	4
α-helix	197-200	4
α-helix	209-220	12
α-helix	234-245	12
α-helix	256-258	3
α-helix	263-265	3
α-helix	275-280	6
α-helix	286-295	10
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-310	5
α-helix	313-316	4
α-helix	320-321	2

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	16-20	5
α-helix	25-27	3
α-helix	31-51	21
α-helix	56-69	14
α-helix	80-95	16
α-helix	101-112	12
α-helix	124-143	20
α-helix	153-162	10
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-207	15
α-helix	212-215	4
α-helix	221-224	4
α-helix	231-247	17
α-helix	252-255	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division protein kinase 9	A	protein	331	Homo sapiens	P50750 (AlphaFold model)
Cyclin-T1	B	protein	260	Homo sapiens	O60563 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3MY1_1 Cell division protein kinase 9 (chains A)
GPAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGF
PITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLV
KFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKN
SQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLA
LISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLD
PAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>3MY1_2 Cyclin-T1 (chains B)
GPEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTI
NTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLP
DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMAT
NSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTH
ELLQILEKTPNRLKRIWNWR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
RFZ	5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole	C12 H12 Cl2 N2 O4	1

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

Primary citation

Halogen bonds form the basis for selective P-TEFb inhibition by DRB. Baumli, S., Endicott, J.A., Johnson, L.N. Chem Biol (2010) 17:931-936. DOI 10.1016/j.chembiol.2010.07.012 · 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
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
4OGR 3.0 Å, crystal structure of P-TEFb complex with AFF4 and Tat

Browse structure collections

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