2W2P Hydrolase Receptor date Nov 03, 2008
title Pcsk9-Deltac D374a Mutant 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: Prodomain, 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
Mutation: 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 0.22589 R_Free 0.27020
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.106 84.106 209.745 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.62 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] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (2w2p.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 2W2P
  • CSU: Contacts of Structural Units for 2W2P
  • Likely Quarternary Molecular Structure file(s) for 2W2P
  • Structure Factors (405 Kb)
  • Retrieve 2W2P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W2P from S2C, [Save to disk]
  • Re-refined 2w2p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W2P 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 2W2P
  • 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 2W2P, from MSDmotif at EBI
  • Fold representative 2w2p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w2p_A] [2w2p_P] [2w2p_E] [2w2p]
  • SWISS-PROT database: [P01130] [Q8NBP7]
  • Domain organization of [LDLR_HUMAN] [PCSK9_HUMAN] by SWISSPFAM
  • Domains found in 2W2P: [EGF_CA] [EGF_like ] by SMART
  • Other resources with information on 2W2P
  • Community annotation for 2W2P 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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