5W0U Hydrolase Dna date May 31, 2017
title Crystal Structure Of Mbp Fused Activation-Induced Cytidine D (Aid) In Complex With Dcmp
authors Q.Qiao, L.Wang, H.Wu
compound source
Molecule: Maltose-Binding Periplasmic Protein,Single-Strand Cytosine Deaminase;
Chain: B, A
Fragment: Unp Residues 27-392,Unp Residues 13-181
Synonym: Mbp,Mmbp,Maltodextrin-Binding Protein,Activation-I Cytidine Deaminase,Aid,Cytidine Aminohydrolase;
Ec: 3.5.4.38
Engineered: Yes
 Organism_scientific: Escherichia Coli O157:H7, Homo Sapiens
Organism_common: Human
Organism_taxid: 83334, 9606
Gene: Male, Z5632, Ecs5017, Aicda, Aid
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Dna (5'-D(Gptptpcpapapgpgpcpcpapg)-3'
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Cptpgpgpcpcptptpgpapapc)-3'
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 2 1
R_factor 0.251 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.005 39.777 153.935 90.00 90.14 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, DCM, GOL, ZN enzyme Hydrolase E.C.3.5.4.38 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • carbohydrate transmembrane t...


    • Primary referenceAID Recognizes Structured DNA for Class Switch Recombination., Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H, Mol Cell. 2017 Aug 3;67(3):361-373.e4. doi: 10.1016/j.molcel.2017.06.034. Epub, 2017 Jul 27. PMID:28757211
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (190 Kb) [Save to disk]
  • Biological Unit Coordinates (5w0u.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (5w0u.pdb2.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 5W0U
  • CSU: Contacts of Structural Units for 5W0U
  • Structure Factors (1065 Kb)
  • Retrieve 5W0U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5W0U from S2C, [Save to disk]
    • View 5W0U 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 5W0U
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5w0u_D] [5w0u_A] [5w0u_G] [5w0u_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5W0U
  • Community annotation for 5W0U at PDBWiki (http://pdbwiki.org)

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