1BE4 Phosphotransferase date May 19, 1998
title Nucleoside Diphosphate Kinase Isoform B From Bovine Retina
authors J.E.Ladner, N.G.Abdulaev, D.L.Kakuev, G.N.Karaschuk, M.Tordova, E.Eisenstein, J.H.Fujiwara, K.D.Ridge, G.L.Gilliland
compound source
Molecule: Nucleoside Diphosphate Transferase
Chain: A, B, C
Ec: 2.7.4.6
Engineered: Yes
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Eye
Tissue: Retina
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.610 128.610 88.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand PCG enzyme Transferase E.C.2.7.4.6 BRENDA
related structures by homologous chain: 1BHN, 1NDL
Gene
Ontology
ChainFunctionProcessComponent
A, C, B
  • deoxyribonuclease activity


  • Primary referenceNucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure., Abdulaev NG, Karaschuk GN, Ladner JE, Kakuev DL, Yakhyaev AV, Tordova M, Gaidarov IO, Popov VI, Fujiwara JH, Chinchilla D, Eisenstein E, Gilliland GL, Ridge KD, Biochemistry 1998 Oct 6;37(40):13958-67. PMID:9760230
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (1be4.pdb1.gz) 161 Kb
  • LPC: Ligand-Protein Contacts for 1BE4
  • CSU: Contacts of Structural Units for 1BE4
  • Likely Quarternary Molecular Structure file(s) for 1BE4
  • Structure Factors (195 Kb)
  • Retrieve 1BE4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BE4 from S2C, [Save to disk]
  • Re-refined 1be4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BE4 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 1BE4
  • 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 1BE4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1be4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1be4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1be4c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1be4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1be4_C] [1be4_B] [1be4] [1be4_A]
  • SWISS-PROT database: [P52175]
  • Domain organization of [NDKA2_BOVIN] by SWISSPFAM
  • Domain found in 1BE4: [NDK ] by SMART
  • Other resources with information on 1BE4
  • Community annotation for 1BE4 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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