2W2M Hydrolase Receptor date Nov 03, 2008
title Wt Pcsk9-Deltac Bound To Wt Egf-A Of Ldlr
authors M.J.Bottomley, A.Cirillo, L.Orsatti, L.Ruggeri, T.S.Fisher, J.C.S R.T.Cummings, R.M.Cubbon, P.Lo Surdo, A.Calzetta, A.Noto, J.Bays M.Mattu, F.Talamo, R.De Francesco, C.P.Sparrow, A.Sitlani, A.Car
compound source
Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: P
Fragment: Propeptide, Residues 53-152
Synonym: Proprotein Convertase Pc9, Subtilisinkexin-Like P Pc9, Neural Apoptosis-Regulated Convertase 1, Narc-1, Pcsk
Ec: 3.4.21.-
Engineered: Yes
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: Petm-10

Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: A
Fragment: Catalytic Domain, Residues 153-451
Synonym: Proprotein Convertase Pc9, Subtilisinkexin-Like P Pc9, Neural Apoptosis-Regulated Convertase 1, Narc-1, Pcsk
Ec: 3.4.21.-
Engineered: Yes

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: Petm-10

Molecule: Low-Density Lipoprotein Receptor
Chain: E
Fragment: Egf-A Domain, Residues 314-393
Synonym: Ldl Receptor
Engineered: Yes

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: Petm-11
symmetry Space Group: P 43 21 2
R_factor 0.21524 R_Free 0.25421
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.004 83.004 211.566 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CA enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


E


Primary referenceStructural and biochemical characterization of the wild type PCSK9/EGF-AB complex and natural FH mutants., Bottomley MJ, Cirillo A, Orsatti L, Ruggeri L, Fisher TS, Santoro JC, Cummings RT, Cubbon RM, Lo Surdo P, Calzetta A, Noto A, Baysarowich J, Mattu M, Talamo F, De Francesco R, Sparrow CP, Sitlani A, Carfi A, J Biol Chem. 2008 Nov 10. PMID:19001363
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (2w2m.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 2W2M
  • CSU: Contacts of Structural Units for 2W2M
  • Likely Quarternary Molecular Structure file(s) for 2W2M
  • Structure Factors (529 Kb)
  • Retrieve 2W2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W2M from S2C, [Save to disk]
  • Re-refined 2w2m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W2M 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 2W2M
  • 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 2W2M, from MSDmotif at EBI
  • Fold representative 2w2m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w2m_A] [2w2m] [2w2m_E] [2w2m_P]
  • SWISS-PROT database: [P01130] [Q8NBP7]
  • Domain organization of [LDLR_HUMAN] [PCSK9_HUMAN] by SWISSPFAM
  • Domains found in 2W2M: [EGF_CA] [EGF_like ] by SMART
  • Other resources with information on 2W2M
  • Community annotation for 2W2M 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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