5JPM Immune System date May 03, 2016
title Structure Of The Complex Of Human Complement C4 With Masp-2 Using Imdff
authors T.I.Croll, G.R.Andersen
compound source
Molecule: Complement C4-A
Chain: A, D
Synonym: Acidic Complement C4,C3 And Pzp-Like Alpha-2-Macro Domain-Containing Protein 2;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Complement C4-A
Chain: B, E
Synonym: Acidic Complement C4,C3 And Pzp-Like Alpha-2-Macro Domain-Containing Protein 2;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Complement C4-A
Chain: C, F
Synonym: Acidic Complement C4,C3 And Pzp-Like Alpha-2-Macro Domain-Containing Protein 2;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Mannan-Binding Lectin Serine Protease 2
Chain: G, I
Synonym: Mbl-Associated Serine Protease 2,Mannose-Binding P Associated Serine Protease 2,Masp-2;
Ec: 3.4.21.104
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Masp2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Mannan-Binding Lectin Serine Protease 2
Chain: H, J
Synonym: Mbl-Associated Serine Protease 2,Mannose-Binding P Associated Serine Protease 2,Masp-2;
Ec: 3.4.21.104
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Masp2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.010 215.010 142.860 90.00 110.11 90.00
method X-Ray Diffractionresolution 3.75 Å
ligand BMA, NAG, TYS enzyme Hydrolase E.C.3.4.21.104 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


F, C


H, J


Primary referenceRe-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4., Croll TI, Andersen GR, Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1006-16. doi:, 10.1107/S2059798316012201. Epub 2016 Aug 18. PMID:27599733
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1417 Kb) [Save to disk]
  • Biological Unit Coordinates (5jpm.pdb1.gz) 706 Kb
  • Biological Unit Coordinates (5jpm.pdb2.gz) 707 Kb
  • LPC: Ligand-Protein Contacts for 5JPM
  • CSU: Contacts of Structural Units for 5JPM
  • Structure Factors (447 Kb)
  • Retrieve 5JPM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JPM from S2C, [Save to disk]
  • Re-refined 5jpm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JPM 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 5JPM
  • 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
  • Fold representative 5jpm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jpm_G] [5jpm_E] [5jpm_F] [5jpm] [5jpm_H] [5jpm_A] [5jpm_B] [5jpm_C] [5jpm_I] [5jpm_D] [5jpm_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JPM: [A2M] [A2M_N_2] [A2M_recep] [ANATO] [C345C] [CCP] [Thiol-ester_cl] [Tryp_SPc ] by SMART
  • Other resources with information on 5JPM
  • Community annotation for 5JPM at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science