2VD6 Lyase date Sep 30, 2007
title Human Adenylosuccinate Lyase In Complex With Its Substrate N6-(1,2-Dicarboxyethyl)-Amp, And Its Products Amp And Fumarate.
authors P.Stenmark, M.Moche, C.Arrowsmith, H.Berglund, R.Busam, R.Collins L.G.Dahlgren, A.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hamma B.M.Hallberg, L.Holmberg-Schiavone, I.Johansson, A.Kallas, T.Ka T.Kotenyova, L.Lehtio, M.Nilsson, T.Nyman, D.Ogg, C.Persson, J.Sa M.Sundstrom, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weig M.Welin, P.Nordlund, Structural Genomics Consortium (Sgc)
compound source
Molecule: Adenylosuccinate Lyase
Chain: A, B, C, D
Fragment: Residues 1-481
Synonym: Adenylosuccinase, Asl, Asase
Ec: 4.3.2.2
Engineered: Yes
Other_details: The Construct Contains A Hexahistidine Tail Linker Sequence In The N-Terminus ( Mhhhhhhssgvdlgtenlyfqs
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pnic-Bsa4
Other_details: Mammalian Gene Collection (Mgc)
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.300 128.100 190.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 2SA, AMP, CL, FMR, FUM, GOL enzyme Lyase E.C.4.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • N6-(1,2-dicarboxyethyl)AMP A...


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (320 Kb) [Save to disk]
  • Biological Unit Coordinates (2vd6.pdb1.gz) 312 Kb
  • LPC: Ligand-Protein Contacts for 2VD6
  • CSU: Contacts of Structural Units for 2VD6
  • Likely Quarternary Molecular Structure file(s) for 2VD6
  • Structure Factors (1971 Kb)
  • Retrieve 2VD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VD6 from S2C, [Save to disk]
  • Re-refined 2vd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VD6 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 2VD6
  • 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 2VD6, from MSDmotif at EBI
  • Fold representative 2vd6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vd6_D] [2vd6] [2vd6_C] [2vd6_A] [2vd6_B]
  • SWISS-PROT database: [P30566]
  • Domain organization of [PUR8_HUMAN] by SWISSPFAM
  • Domain found in 2VD6: [ADSL_C ] by SMART
  • Alignments of the sequence of 2VD6 with the sequences similar proteins can be viewed for 2VD6's classification [PUR8_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PUR8_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VD6
  • Community annotation for 2VD6 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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