2BDG Hydrolase date Oct 20, 2005
title Human Kallikrein 4 Complex With Nickel And P-Aminobenzamidin
authors M.Debela, W.Bode, P.Goettig, Structural Proteomics In Europe (S
compound source
Molecule: Kallikrein-4
Chain: A, B
Fragment: Human Kallikrein 4
Synonym: Prostase, Kallikrein-Like Protein 1, Klk-L1, Ename Serine Proteinase 1;
Ec: 3.4.21.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Klk4, Emsp1, Prss17, Psts
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 4
R_factor 0.169 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
95.680 95.680 38.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CL, NA, NI, PBZ enzyme Hydrolase E.C.3.4.21 BRENDA
A, B

Primary referenceCrystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site., Debela M, Magdolen V, Grimminger V, Sommerhoff C, Messerschmidt A, Huber R, Friedrich R, Bode W, Goettig P, J Mol Biol. 2006 Oct 6;362(5):1094-107. Epub 2006 Aug 3. PMID:16950394
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (2bdg.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (2bdg.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2BDG
  • CSU: Contacts of Structural Units for 2BDG
  • Likely Quarternary Molecular Structure file(s) for 2BDG
  • Structure Factors (165 Kb)
  • Retrieve 2BDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BDG from S2C, [Save to disk]
  • Re-refined 2bdg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BDG 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 2BDG
  • 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 2BDG, from MSDmotif at EBI
  • Fold representative 2bdg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bdg] [2bdg_] [2bdg_A] [2bdg_B]
  • SWISS-PROT database: [Q9Y5K2]
  • Domain organization of [KLK4_HUMAN] by SWISSPFAM
  • Domain found in 2BDG: [Tryp_SPc ] by SMART
  • Other resources with information on 2BDG
  • Community annotation for 2BDG 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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