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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOUSE C5A-DESARG ANAPHYLATOXIN
 
Authors :  L. Yatime, J. A. Schatz-Jakobsen, G. R. Andersen
Date :  06 Mar 14  (Deposition) - 11 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,C  (1x)
Biol. Unit 6:  B (1x),D (1x)
Keywords :  Complement Anaphylatoxin, C5A, Four-Helix Bundle, Gpcr Agonist, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Schatz-Jakobsen, L. Yatime, C. Larsen, S. V. Petersen, A. Klos, G. R. Andersen
Structural And Functional Characterization Of Human And Murine C5A Anaphylatoxins.
Acta Crystallogr. D Biol. V. 70 1704 2014 Crystallogr.
PubMed-ID: 24914981  |  Reference-DOI: 10.1107/S139900471400844X

(-) Compounds

Molecule 1 - COMPLEMENT C5
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: SHUFFLE T7 EXPRESS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 679-754
    Gene: C5, HC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HEMOLYTIC COMPLEMENT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A C 
Biological Unit 6 (1x):  B (1x) D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1FMT15Ligand/IonFORMIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
Biological Unit 3 (1, 7)
No.NameCountTypeFull Name
1FMT7Ligand/IonFORMIC ACID
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
Biological Unit 5 (1, 10)
No.NameCountTypeFull Name
1FMT10Ligand/IonFORMIC ACID
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:705 , HOH A:935 , VAL C:722 , ILE C:724binding site for residue FMT A 801
02AC2SOFTWAREGLY A:725 , PRO A:726 , LEU A:727 , CYS A:728 , HOH A:950 , TYR C:712binding site for residue FMT A 802
03AC3SOFTWARELYS A:701 , GLU A:713binding site for residue FMT A 803
04AC4SOFTWARECYS B:702 , ASP B:705 , VAL D:722 , ILE D:724binding site for residue FMT B 801
05AC5SOFTWAREARG B:721 , HOH B:907 , HOH B:918 , ASN D:710 , ARG D:718 , ARG D:721binding site for residue FMT B 803
06AC6SOFTWAREILE A:724 , ASP C:705 , PHE C:732 , HOH C:933binding site for residue FMT C 801
07AC7SOFTWARETYR A:712 , PRO C:699 , GLY C:725 , PRO C:726 , LEU C:727 , CYS C:728binding site for residue FMT C 802
08AC8SOFTWAREASN C:710 , ARG C:718 , PHE C:732 , HOH C:933binding site for residue FMT C 803
09AC9SOFTWAREHOH C:951 , HOH C:957 , HOH C:967binding site for residue FMT C 805
10AD1SOFTWARELEU C:680 , ARG C:743binding site for residue FMT C 806
11AD2SOFTWARETYR C:694 , LYS C:695 , HIS C:696 , PRO C:699 , LEU C:727binding site for residue FMT C 807
12AD3SOFTWAREILE B:724 , CYS D:702 , ASP D:705binding site for residue FMT D 801
13AD4SOFTWAREGLY B:725 , PRO B:726 , LEU B:727 , CYS B:728 , PHE D:711 , TYR D:712binding site for residue FMT D 802

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:702 -A:728
2A:703 -A:735
3A:715 -A:736
4B:702 -B:728
5B:703 -B:735
6B:715 -B:736
7C:702 -C:728
8C:703 -C:735
9C:715 -C:736
10D:702 -D:728
11D:703 -D:735
12D:715 -D:736

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3B)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3B)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4p3b A 677 GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKE 745
                                   686       696       706       716       726       736         


Chain B from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4p3b B 678 ANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   687       697       707       717       727       737         


Chain C from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4p3b C 677 GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   686       696       706       716       726       736       746


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p3b D 678 ANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKE 745
                                   687       697       707       717       727       737
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4P3B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3B)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CO5_MOUSE | P06684: 4p3a 4wb2 4wb3

(-) Related Entries Specified in the PDB File

4p39 4P39 CONTAINS THE STRUCTURE OF THE HUMAN C5AR ANTAGONIST C5A-A8, A MUTANT FORM OF HUMAN C5A ANAPHYLATOXIN
4p3a 4P3A CONTAINS THE STRUCTURE OF THE INTACT MOUSE C5A ANAPHYLATOXIN