5VLP	Hydrolase	date	Apr 25, 2017
title	Pcsk9 Complex With Ldlr Antagonist Peptide And Fab7g7
authors	C.Eigenbrot, M.Ultsch
compound		source
Molecule: Proprotein Convertase Subtilisinkexin Type 9 Chain: A Synonym: Neural Apoptosis-Regulated Convertase 1,Narc-1,Pro Convertase 9,Pc9,Subtilisinkexin-Like Protease Pc9; Ec: 3.4.21.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pcsk9, Narc1, Psec0052 Expression_system: Cricetulus Griseus Expression_system_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_organ: Ovary
Molecule: Fab7g7 Heavy Chain Chain: H Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Expression_system: Mus Musculus Expression_system_common: Mouse Expression_system_taxid: 10090 Expression_system_cell: Hybridoma
Molecule: Fab7g7 Light Chain Chain: L Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Lc Expression_system: Mus Musculus Expression_system_common: Mouse Expression_system_taxid: 10090 Expression_system_cell: Hybridoma
Molecule: Ldlr Antagonist Peptide Chain: Z Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: I 2 2 2	R_factor 0.171 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 110.865 142.168 239.365 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	ACE, HRG, NA	enzyme	Hydrolase E.C.3.4.21 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists., Zhang Y, Ultsch M, Skelton NJ, Burdick DJ, Beresini MH, Li W, Kong-Beltran M, Peterson A, Quinn J, Chiu C, Wu Y, Shia S, Moran P, Di Lello P, Eigenbrot C, Kirchhofer D, Nat Struct Mol Biol. 2017 Aug 21. doi: 10.1038/nsmb.3453. PMID:28825733

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (337 Kb) [Save to disk] Biological Unit Coordinates (5vlp.pdb1.gz) 329 Kb LPC: Ligand-Protein Contacts for 5VLP CSU: Contacts of Structural Units for 5VLP Structure Factors (1505 Kb) Retrieve 5VLP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5VLP from S2C, [Save to disk]

View 5VLP 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 5VLP

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5vlp_H] [5vlp_L] [5vlp_Z] [5vlp_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5VLP

Community annotation for 5VLP at PDBWiki (http://pdbwiki.org)

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