3BPS Hydrolase Lipid Transport date Dec 19, 2007
title Pcsk9:Egf-A Complex
authors H.J.Kwon
compound source
Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: P
Fragment: Prodomain, Unp Residues 53-152
Synonym: Proprotein Convertase Pc9, Subtilisinkexin-Like P Pc9, Neural Apoptosis-Regulated Convertase 1, Narc-1;
Ec: 3.4.21.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcsk9, Narc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hek293s

Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: A
Fragment: Catalytic Domain, Unp Residues 153-692
Synonym: Proprotein Convertase Pc9, Subtilisinkexin-Like P Pc9, Neural Apoptosis-Regulated Convertase 1, Narc-1;
Ec: 3.4.21.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcsk9, Narc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hek293s

Molecule: Low-Density Lipoprotein Receptor
Chain: E
Fragment: Egf-Like 1, Egf-Like 2 Domains, Unp Residues 314-
Synonym: Ldl Receptor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ldlr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.203 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.952 116.952 134.878 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand CA enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


E


Primary referenceMolecular basis for LDL receptor recognition by PCSK9., Kwon HJ, Lagace TA, McNutt MC, Horton JD, Deisenhofer J, Proc Natl Acad Sci U S A. 2008 Feb 4;. PMID:18250299
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (3bps.pdb1.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 3BPS
  • CSU: Contacts of Structural Units for 3BPS
  • Likely Quarternary Molecular Structure file(s) for 3BPS
  • Structure Factors (274 Kb)
  • Retrieve 3BPS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BPS from S2C, [Save to disk]
  • Re-refined 3bps structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BPS 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 3BPS
  • 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 3BPS, from MSDmotif at EBI
  • Fold representative 3bps from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bps] [3bps_P] [3bps_A] [3bps_E]
  • SWISS-PROT database: [P01130] [Q8NBP7]
  • Domain organization of [LDLR_HUMAN] [PCSK9_HUMAN] by SWISSPFAM
  • Domains found in 3BPS: [EGF_CA] [EGF_like ] by SMART
  • Other resources with information on 3BPS
  • Community annotation for 3BPS 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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