3BLR: Human CDK9/cyclinT1

Crystal Structure of Human CDK9/cyclinT1 in complex with Flavopiridol. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 Jul 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,551
Mol. weight: 68.86 kDa
Ligands: PO4, CPB
Released: 1 Jul 2008

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

Secondary structure: helices and β-sheets

3BLR contains 34 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: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-18	3
β-strand	19-26	8	2
β-strand	33-38	6	2
β-strand	44-49	6	2
α-helix	50-51	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	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	275-279	5
α-helix	286-295	10
α-helix	300-302	3
α-helix	304-305	2
α-helix	306-310	5
α-helix	313-315	3
α-helix	320-321	2

Chain B: 16 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	80-94	15
α-helix	101-112	12
α-helix	124-143	20
α-helix	153-156	4
α-helix	158-160	3
α-helix	168-184	17
α-helix	187-189	3
α-helix	193-208	16
α-helix	210-215	6
α-helix	221-224	4
α-helix	231-247	17
α-helix	251-254	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

>3BLR_1 Cell division protein kinase 9 (chains A)
GPAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGF
PITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLV
KFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKN
SQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLA
LISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLD
PAQRIDSDDALNHDFFWSDPMPSDLKGMLST

Sequence of entity 2 (B), FASTA

>3BLR_2 Cyclin-T1 (chains B)
GPEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTI
NTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEGQPKKLEHVIKVAHTCLHPQESLP
DTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMAT
NSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTH
ELLQILEKTPNRLKRIWNWR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
CPB	2-(2-chloro-phenyl)-5,7-dihydroxy-8-(3-hydroxy-1-methyl-piperidin-4-yl)-4H-benz…	C21 H20 Cl N O5	1

Primary citation

The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation. Baumli, S., Lolli, G., Lowe, E.D. et al. EMBO J (2008) 27:1907-1918. DOI 10.1038/emboj.2008.121 · 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
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
4OGR 3.0 Å, crystal structure of P-TEFb complex with AFF4 and Tat

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