Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOUSE C5A 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 :  1.40
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,B  (1x)
Biol. Unit 6:  C,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 679-755
    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): AB  
Biological Unit 6 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1FMT16Ligand/IonFORMIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1FMT7Ligand/IonFORMIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
Biological Unit 5 (1, 10)
No.NameCountTypeFull Name
1FMT10Ligand/IonFORMIC ACID
Biological Unit 6 (1, 6)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:702 , ASP A:705 , HOH A:935 , VAL B:722 , ILE B:724binding site for residue FMT A 801
02AC2SOFTWAREGLY A:725 , PRO A:726 , LEU A:727 , CYS A:728 , HOH A:962 , PHE B:711 , TYR B:712binding site for residue FMT A 802
03AC3SOFTWAREASN A:710 , GLU A:713 , HOH A:958 , HOH A:961binding site for residue FMT A 803
04AC4SOFTWAREILE A:724 , ASP B:705 , HOH B:951binding site for residue FMT B 801
05AC5SOFTWAREARG A:721 , ASN B:710 , ARG B:718 , ARG B:721 , PHE B:732 , HOH B:951 , HOH B:952binding site for residue FMT B 802
06AC6SOFTWARETYR A:712 , PRO B:699 , GLY B:725 , PRO B:726 , LEU B:727 , CYS B:728binding site for residue FMT B 803
07AC7SOFTWARETYR B:694 , LYS B:695 , HIS B:696 , LEU B:727binding site for residue FMT B 804
08AC8SOFTWARELEU B:680 , ARG B:743 , HOH B:959 , HOH B:991binding site for residue FMT B 805
09AC9SOFTWAREHOH A:947 , ARG B:708binding site for residue FMT B 806
10AD1SOFTWAREGLU B:689 , HOH B:901 , ARG C:730binding site for residue FMT B 807
11AD2SOFTWAREASP C:705 , HOH C:947 , ILE D:724binding site for residue FMT C 801
12AD3SOFTWARELEU C:683 , ARG C:743 , HOH C:981binding site for residue FMT C 802
13AD4SOFTWAREILE C:724 , ASP D:705 , PHE D:732 , HOH D:937binding site for residue FMT D 801
14AD5SOFTWAREARG C:721 , ASN D:710 , ARG D:718 , PHE D:732 , HOH D:937 , HOH D:941binding site for residue FMT D 802
15AD6SOFTWAREGLY C:725 , PRO C:726 , LEU C:727 , CYS C:728 , TYR D:712 , HOH D:910binding site for residue FMT D 803
16AD7SOFTWAREALA D:678 , LEU D:683 , ARG D:743 , HOH D:946binding site for residue FMT D 804

(-) 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 4P3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3A)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3A)

(-) 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:70
                                                                                                      
               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
                 4p3a A 677 GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   686       696       706       716       726       736       746


Chain B 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
                 4p3a B 677 GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKE 745
                                   686       696       706       716       726       736         


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p3a C 678 ANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKE 745
                                   687       697       707       717       727       737        


Chain D 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
                 4p3a D 678 ANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKES 746
                                   687       697       707       717       727       737
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4P3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3A)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4p3a)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4p3a
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CO5_MOUSE | P06684
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CO5_MOUSE | P06684
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CO5_MOUSE | P06684: 4p3b 4wb2 4wb3

(-) Related Entries Specified in the PDB File

4p39 4P39 CONTAINS THE STRUCTURE OF THE HUMAN C5AR ANTAGONIST, C5A-A8, DERIVED FROM C5A ANAPHYLATOXIN
4p3b