5M6W Immune System date Oct 26, 2016
title Properdin In Complex With Alternative Pathway C3 Convertase
authors D.V.Pedersen, G.R.Andersen
compound source
Molecule: Complement C3
Chain: A, G
Fragment: Beta Chain, Unp Residues 23-667
Synonym: C3 And Pzp-Like Alpha-2-Macroglobulin Domain-Conta Protein 1;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Complement C3
Chain: B, H
Fragment: Alpha Chain, Unp Residues 751-1663
Synonym: C3 And Pzp-Like Alpha-2-Macroglobulin Domain-Conta Protein 1;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Complement Factor B
Chain: J, L
Fragment: Bb Fragment, Unp Residues 260-764
Synonym: C3c5 Convertase,Glycine-Rich Beta Glycoprotein,Gb Properdin Factor B;
Ec: 3.4.21.47
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cfb, Bf, Bfd
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293

Molecule: Staphylococcal Complement Inhibitor
Chain: N, Q
Synonym: Scin
Engineered: Yes

Organism_scientific: Staphylococcus Aureus Subsp. Aureus Mr
Organism_taxid: 282458
Gene: Scn, Sar2035
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.289 R_Free 0.322
crystal
cell
length a length b length c angle alpha angle beta angle gamma
634.870 121.980 264.420 90.00 112.91 90.00
method X-Ray Diffractionresolution 6.00 Å
ligand BMA, MAN, MG, NAG enzyme Hydrolase E.C.3.4.21.47 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, G


B, H


J, L


N, Q


Primary referenceFunctional and structural insight into properdin control of complement alternative pathway amplification., Pedersen DV, Roumenina L, Jensen RK, Gadeberg TA, Marinozzi C, Picard C, Rybkine T, Thiel S, Sorensen UB, Stover C, Fremeaux-Bacchi V, Andersen GR, EMBO J. 2017 Mar 6. pii: e201696173. doi: 10.15252/embj.201696173. PMID:28264884
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1523 Kb) [Save to disk]
  • Biological Unit Coordinates (5m6w.pdb1.gz) 1511 Kb
  • LPC: Ligand-Protein Contacts for 5M6W
  • CSU: Contacts of Structural Units for 5M6W
  • Structure Factors (1363 Kb)
  • Retrieve 5M6W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M6W from S2C, [Save to disk]
  • Re-refined 5m6w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5M6W 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 5M6W
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5m6w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5m6w] [5m6w_J] [5m6w_L] [5m6w_Q] [5m6w_H] [5m6w_N] [5m6w_G] [5m6w_A] [5m6w_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5M6W
  • Community annotation for 5M6W at PDBWiki (http://pdbwiki.org)

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