Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE OLIGOMERISATION DOMAIN OF C4B-BINDING PROTEIN FROM GALLUS GALLUS
 
Authors :  J. J. E. Caesar, F. Hill, S. M. Lea
Date :  01 Apr 11  (Deposition) - 18 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Immune System, Complement System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. E. Caesar, F. Hill, S. M. Lea
Crystal Structure Of The Oligomerisation Domain Of C4B-Binding Protein From Gallus Gallus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - C4B BINDING PROTEIN
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41(DE3)
    Fragment: OLIGOMERISATION DOMAIN, RESIDUES 395-457
    Mutation: YES
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 30)

Asymmetric/Biological Unit (2, 30)
No.NameCountTypeFull Name
1ACT11Ligand/IonACETATE ION
2EDO19Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS C:433 , LYS D:433 , GLU D:437 , EDO D:1449BINDING SITE FOR RESIDUE EDO D1448
02AC2SOFTWAREGLU C:430 , GLU D:430 , EDO D:1448BINDING SITE FOR RESIDUE EDO D1449
03AC3SOFTWAREGLU F:430 , GLU G:430 , LEU G:434 , HOH G:2008BINDING SITE FOR RESIDUE EDO G1460
04AC4SOFTWARELYS E:433 , GLU F:430 , LYS F:433 , LEU F:434 , GLU F:437 , HOH F:2012BINDING SITE FOR RESIDUE EDO F1448
05AC5SOFTWAREGLN A:412 , THR A:422 , ASP B:424 , EDO B:1450 , PRO D:421BINDING SITE FOR RESIDUE EDO B1447
06AC6SOFTWAREGLU A:430 , GLU B:430 , LEU B:434 , HOH B:2008BINDING SITE FOR RESIDUE EDO B1448
07AC7SOFTWAREGLN B:412 , SER B:416 , THR B:422 , EDO B:1451 , ACT B:1454 , HIS C:419BINDING SITE FOR RESIDUE EDO B1449
08AC8SOFTWAREGLU B:423 , EDO B:1451 , EDO B:1452 , GLU C:423 , ASP C:424 , THR C:427 , EDO C:1461 , HOH C:2006BINDING SITE FOR RESIDUE EDO C1460
09AC9SOFTWAREGLU G:444BINDING SITE FOR RESIDUE EDO G1461
10BC1SOFTWARELYS F:440 , GLU G:437 , LYS G:440 , LEU G:441 , GLU G:444BINDING SITE FOR RESIDUE EDO G1462
11BC2SOFTWAREGLU A:423 , GLU B:423 , ASP B:424 , THR B:427 , EDO B:1447 , HOH B:2012 , GLU D:423BINDING SITE FOR RESIDUE EDO B1450
12BC3SOFTWARELYS E:426 , GLU F:423 , LYS F:426 , THR F:427 , GLU F:430BINDING SITE FOR RESIDUE EDO F1449
13BC4SOFTWAREPRO E:421 , THR E:422 , PRO G:421 , THR G:422 , ACT G:1464 , HOH G:2009BINDING SITE FOR RESIDUE EDO G1463
14BC5SOFTWAREGLU A:423 , ASP A:424 , THR A:427 , GLU E:423 , HOH E:2005 , GLU G:423 , ACT G:1464BINDING SITE FOR RESIDUE EDO A1459
15BC6SOFTWAREGLN B:412 , THR B:422 , EDO B:1449 , EDO B:1452 , PRO C:421 , ASP C:424 , LEU C:428 , EDO C:1460BINDING SITE FOR RESIDUE EDO B1451
16BC7SOFTWAREASP G:424BINDING SITE FOR RESIDUE EDO F1450
17BC8SOFTWARELYS B:426 , GLU C:423 , LYS C:426 , THR C:427 , GLU C:430 , EDO C:1460BINDING SITE FOR RESIDUE EDO C1461
18BC9SOFTWAREPRO B:421 , THR B:422 , GLU B:423 , EDO B:1452 , ACT B:1454 , THR C:422 , GLU C:423 , ACT C:1463 , HOH C:2013 , THR D:427BINDING SITE FOR RESIDUE EDO C1462
19CC1SOFTWARETHR B:422 , GLU B:423 , EDO B:1451 , ACT B:1454 , PRO C:421 , THR C:422 , GLU C:423 , THR C:427 , EDO C:1460 , EDO C:1462BINDING SITE FOR RESIDUE EDO B1452
20CC2SOFTWARELEU C:457 , GLY C:459 , GLU D:407 , ARG E:432 , LYS F:442BINDING SITE FOR RESIDUE ACT E1459
21CC3SOFTWAREVAL D:404 , ARG F:432 , PHE F:435BINDING SITE FOR RESIDUE ACT F1451
22CC4SOFTWAREGLU A:407 , ARG B:432 , LYS C:442BINDING SITE FOR RESIDUE ACT B1453
23CC5SOFTWAREVAL B:404 , ILE D:431 , ARG D:432 , PHE D:435BINDING SITE FOR RESIDUE ACT D1450
24CC6SOFTWAREPRO B:421 , GLN C:412 , THR C:422 , EDO C:1462 , ASP D:424 , LEU D:428BINDING SITE FOR RESIDUE ACT C1463
25CC7SOFTWAREPRO A:421 , THR A:422 , PRO D:421 , THR D:422 , HOH D:2011BINDING SITE FOR RESIDUE ACT D1451
26CC8SOFTWAREARG A:432 , PHE A:435 , VAL F:404BINDING SITE FOR RESIDUE ACT A1460
27CC9SOFTWAREPRO B:421 , THR B:422 , EDO B:1449 , EDO B:1452 , PRO C:421 , THR C:422 , EDO C:1462BINDING SITE FOR RESIDUE ACT B1454
28DC1SOFTWAREGLN E:412 , THR E:422 , ASP F:424 , LEU F:428 , PRO G:421BINDING SITE FOR RESIDUE ACT E1460
29DC2SOFTWARELYS B:426 , GLU B:430BINDING SITE FOR RESIDUE ACT B1455
30DC3SOFTWAREASP A:424 , LEU A:428 , EDO A:1459 , PRO E:421 , GLN G:412 , THR G:422 , EDO G:1463BINDING SITE FOR RESIDUE ACT G1464

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:405 -B:418
2A:418 -G:405
3B:405 -C:418
4C:405 -D:418
5D:405 -E:418
6E:405 -F:418
7F:405 -G:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YF2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YF2)

(-) Exons   (0, 0)

(no "Exon" information available for 2YF2)

(-) Sequences/Alignments

Asymmetric/Biological 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:57
                                                                                         
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 2yf2 A 402 ADVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQGLSKEFLEHILH 458
                                   411       421       431       441       451       


Chain B from PDB  Type:PROTEIN  Length:46
                                                                              
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 2yf2 B 401 DADVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQ 446
                                   410       420       430       440      


Chain C from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2yf2 C 402 ADVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQGLSKEFLEHILHG 459
                                   411       421       431       441       451        


Chain D from PDB  Type:PROTEIN  Length:46
                                                                              
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 2yf2 D 402 ADVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQG 447
                                   411       421       431       441      


Chain E from PDB  Type:PROTEIN  Length:55
                                                                                       
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 2yf2 E 404 VCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQGLSKEFLEHILH 458
                                   413       423       433       443       453     


Chain F from PDB  Type:PROTEIN  Length:45
                                                                             
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 2yf2 F 403 DVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQG 447
                                   412       422       432       442     


Chain G from PDB  Type:PROTEIN  Length:57
                                                                                         
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 2yf2 G 403 DVCGEVAYIQSVVSDCHVPTEDVKTLLEIRKLFLEIQKLKVELQGLSKEFLEHILHG 459
                                   412       422       432       442       452
   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 2YF2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YF2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YF2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2YF2)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yf2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2yf2
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2YF2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YF2)