4OV6 Hydrolase Protein Binding date Feb 20, 2014
title Crystal Structure Of Pcsk9(53-451) With Adnectin
authors J.A.Khan
compound source
Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: A, D
Fragment: Prodomain (Unp Residues 60-152)
Synonym: Pcsk9, Neural Apoptosis-Regulated Convertase 1, Na Proprotein Convertase 9, Pc9, Subtilisinkexin-Like Proteas
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcsk9, Narc1, Psec0052
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pachlt

Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: B, E
Fragment: Catalytic Domain (Unp Residues 153-446)
Synonym: Pcsk9, Neural Apoptosis-Regulated Convertase 1, Na Proprotein Convertase 9, Pc9, Subtilisinkexin-Like Proteas
Ec: 3.4.21.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcsk9, Narc1, Psec0052
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pachlt

Molecule: Adnectin
Chain: F, G
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_vector_type: Plasmid
Expression_system_plasmid: Pet-9d
symmetry Space Group: P 21 21 21
R_factor 0.199 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.200 118.600 168.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.69 Å
ligand EDO, PG4 enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E, B


Primary referencePharmacologic Profile of the Adnectin BMS-962476, a Small Protein Biologic Alternative to PCSK9 Antibodies for LDL Lowering., Mitchell T, Chao G, Sitkoff D, Lo F, Monshizadegan H, Meyers D, Low S, Russo K, DiBella R, Denhez F, Gao M, Myers J, Duke G, Witmer M, Miao B, Ho SP, Khan J, Parker RA, J Pharmacol Exp Ther. 2014 Jun 10. pii: jpet.114.214221. PMID:24917546
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (4ov6.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (4ov6.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 4OV6
  • CSU: Contacts of Structural Units for 4OV6
  • Structure Factors (2303 Kb)
  • Retrieve 4OV6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OV6 from S2C, [Save to disk]
  • Re-refined 4ov6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OV6 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 4OV6
  • 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 4OV6, from MSDmotif at EBI
  • Fold representative 4ov6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ov6] [4ov6_B] [4ov6_A] [4ov6_D] [4ov6_G] [4ov6_F] [4ov6_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4OV6: [FN3 ] by SMART
  • Other resources with information on 4OV6
  • Community annotation for 4OV6 at PDBWiki (http://pdbwiki.org)

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