3DH1 Hydrolase date Jun 16, 2008
title Crystal Structure Of Human Trna-Specific Adenosine-34 Deamin Subunit Adat2
authors M.Welin, L.Tresaugues, J.Andersson, C.H.Arrowsmith, H.Berglund, R L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Ham A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, L.Lehtio, M.M M.E.Nilsson, T.Nyman, K.Olesen, C.Persson, J.Sagemark, H.Schuele A.G.Thorsell, S.Van Der Berg, M.Wisniewska, M.Wikstrom, P.Nordl Structural Genomics Consortium (Sgc)
compound source
Molecule: Trna-Specific Adenosine Deaminase 2
Chain: A, B, C, D
Fragment: Residues 20-185
Synonym: Trna-Specific Adenosine-34 Deaminase Subunit Adat2 Deaminase Domain-Containing Protein 1;
Ec: 3.5.4.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Adat2, Deadc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) R3 Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
47.530 103.120 77.590 90.00 97.60 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme Hydrolase E.C.3.5.4 BRENDA
note 3DH1 is a representative structure
A, D, C, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (3dh1.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (3dh1.pdb2.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3DH1
  • CSU: Contacts of Structural Units for 3DH1
  • Likely Quarternary Molecular Structure file(s) for 3DH1
  • Structure Factors (271 Kb)
  • Retrieve 3DH1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DH1 from S2C, [Save to disk]
  • Re-refined 3dh1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DH1 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 3DH1
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3DH1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f3dh1, region H:1-121 [Jmol] [rasmolscript] [script source]
        - Domain d1m3dh1, region H:4-114 [Jmol] [rasmolscript] [script source]
  • Fold representative 3dh1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dh1_D] [3dh1_A] [3dh1_C] [3dh1] [3dh1_B]
  • SWISS-PROT database: [Q7Z6V5]
  • Domain organization of [ADAT2_HUMAN] by SWISSPFAM
  • Other resources with information on 3DH1
  • Community annotation for 3DH1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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