3GHM Hydrolase date Mar 04, 2009
title Crystal Structure Of The Exosite-Containing Fragment Of Huma (Form-1)
authors M.Akiyama, S.Takeda, K.Kokame, J.Takagi, T.Miyata
compound source
Molecule: A Disintegrin And Metalloproteinase With Thrombos Motifs 13;
Chain: A
Fragment: Dtcs Domains
Synonym: Adamts-13, Adam-Ts 13, Adam-Ts13, Von Willebrand F Cleaving Protease, Vwf-Cleaving Protease, Vwf-Cp;
Ec: 3.4.24.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adamts13
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Lec 2.3.8.1
Expression_system_cell_line: Cho Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcm-Nidsp
symmetry Space Group: C 1 2 1
R_factor 0.243 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.667 52.914 76.218 90.00 111.35 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand BGC, FUC, NAG enzyme Hydrolase E.C.3.4.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (3ghm.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3GHM
  • CSU: Contacts of Structural Units for 3GHM
  • Structure Factors (132 Kb)
  • Retrieve 3GHM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GHM from S2C, [Save to disk]
  • Re-refined 3ghm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GHM 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 3GHM
  • 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 3GHM, from MSDmotif at EBI
  • Fold representative 3ghm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ghm] [3ghm_A]
  • SWISS-PROT database: [Q76LX8]
  • Domain organization of [ATS13_HUMAN] by SWISSPFAM
  • Domains found in 3GHM: [ACR] [TSP1 ] by SMART
  • Alignments of the sequence of 3GHM with the sequences similar proteins can be viewed for 3GHM's classification [ATS13_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 [ATS13_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3GHM
  • Community annotation for 3GHM 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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