4A09 Dna-Binding Protein Dna date Sep 08, 2011
title Structure Of Hsddb1-Drddb2 Bound To A 15 Bp Cpd-Duplex (Puri Position) At 3.1 A Resolution (Cpd 2)
authors A.Scrima, E.S.Fischer, S.Iwai, H.Gut, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A
Synonym: Ddb P127 Subunit, Dna Damage-Binding Protein A, Dd Damage-Specific Dna-Binding Protein 1, Hbv X-Associated Pro Xap-1, Uv-Damaged Dna-Binding Factor, Uv-Damaged Dna-Bindin 1, Uv-Ddb 1, Xpe-Binding Factor, Xpe-Bf, Xeroderma Pigmento E-Complementing Protein, Xpce;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: Dna Damage-Binding Protein 2
Chain: B
Fragment: Residues 60-423
Synonym: Damage-Specific Dna-Binding Protein 2
Engineered: Yes

Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: 5'-D(Gpgptpgpapapap(Ttd)Papgpcpapgp
Chain: G
Engineered: Yes
Other_details: Damaged Strand. Contains Cyclobutane Pyrimid (Cpd);

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Cpcptpgpcptpcpcptptptpcpapcpc
Chain: H
Engineered: Yes
Other_details: Undamaged Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.245 R_Free 0.308
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.650 122.940 154.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand CA, TTD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceThe Molecular Basis of CRL4(DDB2/CSA) Ubiquitin Ligase Architecture, Targeting, and Activation., Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F, Iwai S, Gut H, Sugasawa K, Thoma NH, Cell. 2011 Nov 23;147(5):1024-39. PMID:22118460
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (4a09.pdb1.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 4A09
  • CSU: Contacts of Structural Units for 4A09
  • Structure Factors (552 Kb)
  • Retrieve 4A09 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A09 from S2C, [Save to disk]
  • Re-refined 4a09 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A09 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4A09
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4A09, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a09_G] [4a09_B] [4a09_A] [4a09_H] [4a09]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4A09: [WD40 ] by SMART
  • Other resources with information on 4A09
  • Community annotation for 4A09 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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