2XTJ Hydrolase Antibody date Oct 10, 2010
title The Crystal Structure Of Pcsk9 In Complex With 1d05 Fab
authors S.Di Marco, C.Volpari, A.Carfi
compound source
Molecule: Proprotein Convertase Subtilisinkexin Type 9
Chain: A
Fragment: Catalytic Domain, Residues 153-451
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
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm-10

Molecule: Fab From A Human Monoclonal Antibody, 1d05
Chain: B
Fragment: Light Chain Variable Domain, Residues 1-107
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmorphx9
Other_details: Human Combinatorial Antibody Phage Display L

Molecule: Fab From A Human Monoclonal Antibody, 1d05
Chain: C
Fragment: Light Chain Constant Domain, Residues 108-213
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pmorphx9
Other_details: Human Combinatorial Antibody Phage Display L

Molecule: Fab From A Human Monoclonal Antibody, 1d05
Chain: D
Fragment: Heavy Chain Variable Domain, Residues 1-131
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmorphx9
Other_details: Human Combinatorial Antibody Phage Display L

Molecule: Fab From A Human Monoclonal Antibody, 1d05
Chain: E
Fragment: Heavy Chain Constant Domain, Residues 132-233
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmorphx9
Other_details: Human Combinatorial Antibody Phage Display L

Molecule: Proprotein Convertase Subtilisin-Kexin Type 9
Chain: P
Fragment: Prodomain, Residues 53-152
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
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm-10
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.589 67.834 250.860 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CA enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA proprotein convertase subtilisin-like/kexin type 9 (PCSK9)-binding antibody that structurally mimics the EGF(A) domain of LDL-receptor reduces free circulating PCSK9 and LDL-cholesterol., Ni YG, Di Marco S, Condra JH, Peterson LB, Wang W, Wang F, Pandit S, Hammond HA, Rosa R, Cummings RT, Wood DD, Liu X, Bottomley MJ, Shen X, Cubbon RM, Wang SP, Johns DG, Volpari C, Hamuro L, Chin J, Huang L, Zhao JZ, Vitelli S, Haytko P, Wisniewski D, Mitnaul LJ, Sparrow CP, Hubbard B, Carfi A, Sitlani A, J Lipid Res. 2010 Oct 19. PMID:20959675
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (2xtj.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 2XTJ
  • CSU: Contacts of Structural Units for 2XTJ
  • Structure Factors (1699 Kb)
  • Retrieve 2XTJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XTJ from S2C, [Save to disk]
  • Re-refined 2xtj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XTJ 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 2XTJ
  • 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 2XTJ, from MSDmotif at EBI
  • Fold representative 2xtj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xtj_D] [2xtj] [2xtj_E] [2xtj_A] [2xtj_B] [2xtj_P] [2xtj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XTJ: [IGc1] [IGv ] by SMART
  • Other resources with information on 2XTJ
  • Community annotation for 2XTJ 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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