5ZDZ Dna Binding Protein date Feb 25, 2018
title Hairpin Forming Complex, Rag12-Nicked 12rss23rss Complex I
authors M.S.Kim, W.Chuenchor, X.Chen, M.Gellert, W.Yang
compound source
Molecule: Mouse Rag1
Chain: A, C
Fragment: Unp Residues 384-1008
Synonym: Rag-1
Ec: 3.1.-.-,2.3.2.27
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t

Molecule: Mouse Rag2
Chain: B, D
Fragment: Unp Residues 1-387
Synonym: Rag-2
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag2, Rag-2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t

Molecule: Hmgb1 A-B Box
Chain: N
Fragment: Unp Residues 1-163
Synonym: High Mobility Group Protein 1,Hmg-1
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Hmgb1, Hmg-1, Hmg1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Tpaptpcptpgpgpcpcptpgptpcp 3');
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (54-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (30-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (39-Mer)
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Chain L
Chain: L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Chain M
Chain: M
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.450 109.000 156.050 90.00 114.28 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CA, EDO, K, ZN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


N


Primary referenceCracking the DNA Code for V(D)J Recombination., Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W, Mol Cell. 2018 Apr 19;70(2):358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Epub, 2018 Apr 5. PMID:29628308
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (421 Kb) [Save to disk]
  • Biological Unit Coordinates (5zdz.pdb1.gz) 221 Kb
  • Biological Unit Coordinates (5zdz.pdb2.gz) 198 Kb
  • LPC: Ligand-Protein Contacts for 5ZDZ
  • CSU: Contacts of Structural Units for 5ZDZ
  • Structure Factors (3241 Kb)
  • Retrieve 5ZDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZDZ from S2C, [Save to disk]
  • View 5ZDZ 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 5ZDZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5zdz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5zdz_N] [5zdz_M] [5zdz_D] [5zdz_F] [5zdz_I] [5zdz_J] [5zdz_B] [5zdz_L] [5zdz_C] [5zdz_A] [5zdz_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ZDZ
  • Community annotation for 5ZDZ at PDBWiki (http://pdbwiki.org)

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