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PDBsum entry 3my1

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protein ligands Protein-protein interface(s) links
Transcription/protein binding/inhibitor PDB id
3my1
Jmol
Contents
Protein chains
315 a.a. *
252 a.a. *
Ligands
PO4
GOL ×5
RFZ
Waters ×36
* Residue conservation analysis
PDB id:
3my1
Name: Transcription/protein binding/inhibitor
Title: Structure of cdk9/cyclint1 in complex with drb
Structure: Cell division protein kinase 9. Chain: a. Fragment: unp residues 2-330. Synonym: cyclin-dependent kinase 9, serine/threonine-protei pitalre, cell division cycle 2-like protein kinase 4, c-2k. Engineered: yes. Cyclin-t1. Chain: b. Fragment: unp residues 2-259.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cdc2l4, cdk9. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: ccnt1.
Resolution:
2.80Å     R-factor:   0.175     R-free:   0.214
Authors: S.Baumli,L.N.Johnson
Key ref: S.Baumli et al. (2010). Halogen bonds form the basis for selective P-TEFb inhibition by DRB. Chem Biol, 17, 931-936. PubMed id: 20851342
Date:
09-May-10     Release date:   29-Sep-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P50750  (CDK9_HUMAN) -  Cyclin-dependent kinase 9
Seq:
Struc:
372 a.a.
315 a.a.*
Protein chain
Pfam   ArchSchema ?
O60563  (CCNT1_HUMAN) -  Cyclin-T1
Seq:
Struc:
 
Seq:
Struc:
726 a.a.
252 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.2.7.11.22  - Cyclin-dependent kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = RFZ)
matches with 46.88% similarity
+ phosphoprotein
   Enzyme class 3: Chain A: E.C.2.7.11.23  - [RNA-polymerase]-subunit kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
ATP
+ [DNA-directed RNA polymerase]
=
ADP
Bound ligand (Het Group name = RFZ)
matches with 46.88% similarity
+ [DNA-directed RNA polymerase] phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   4 terms 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     5 terms  

 

 
    reference    
 
 
Chem Biol 17:931-936 (2010)
PubMed id: 20851342  
 
 
Halogen bonds form the basis for selective P-TEFb inhibition by DRB.
S.Baumli, J.A.Endicott, L.N.Johnson.
 
  ABSTRACT  
 
No abstract given.