PDBsum entry 8buf

Ligase

PDB id: 8buf

Contents

Protein chains

826 a.a.

319 a.a.

247 a.a.

Ligands

SO4 ×46

RW6 ×3

PDB id:

8buf

Name:

Ligase

Title:

Structure of ddb1 bound to z12-engaged cdk12-cyclin k

Structure:

DNA damage-binding protein 1. Chain: a, d, g. Synonym: ddb p127 subunit,DNA damage-binding protein a,ddba,damage- specific DNA-binding protein 1,hbv x-associated protein 1,xap-1,uv- damaged DNA-binding factor,uv-damaged DNA-binding protein 1,uv-ddb 1, xpe-binding factor,xpe-bf,xeroderma pigmentosum group e-complementing protein,xpce. Engineered: yes. Cyclin-dependent kinase 12.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ddb1, xap1. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Gene: cdk12, crk7, crkrs, kiaa0904. Gene: ccnk, cpr4. Expression_system_taxid: 7111

Resolution:

3.30Å R-factor: 0.186 R-free: 0.220

Authors:

Z.Kozicka,G.Kempf,G.Petzold,N.H.Thoma

Key ref:

Z.Kozicka et al. Structure of ddb1 bound to z11-Engaged cdk12-Cyclin k. To be published, . PubMed id: 37679459

Date:

30-Nov-22 Release date: 13-Sep-23

Protein chains

Q16531  (DDB1_HUMAN) -  DNA damage-binding protein 1 from Homo sapiens

Seq: 1140 a.a.

Struc: 826 a.a.

Protein chains

Q9NYV4  (CDK12_HUMAN) -  Cyclin-dependent kinase 12 from Homo sapiens

Seq: 1490 a.a.

Struc: 319 a.a.*

Protein chains

O75909  (CCNK_HUMAN) -  Cyclin-K from Homo sapiens

Seq: 580 a.a.

Struc: 247 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains B, E, H: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 3: Chains B, E, H: E.C.2.7.11.23 - [RNA-polymerase]-subunit kinase.
• Reaction: [DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] + ADP + H⁺

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