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 FATTY ACID BINDING DEGV FAMILY PROTEIN SAG1342 FROM STREPTOCOCCUS AGALACTIAE
 
Authors :  C. Chang, R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Struct Genomics (Mcsg)
Date :  18 Feb 10  (Deposition) - 02 Mar 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Psi-2, Mcsg, Structural Genomics, Fatty Acid Binding, Protein Structure Initiative, Midwest Center For Structural Genomics, Structure Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, R. Wu, S. Clancy, A. Joachimiak
Crystal Structure Of Fatty Acid Binding Degv Family Protein Sag1342 From Streptococcus Agalactiae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEGV FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SAG1342
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 208435
    Strain: 2603V/R

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ELA1Ligand/Ion9-OCTADECENOIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:61 , SER A:62 , GLN A:63 , ILE A:89 , ILE A:93 , SER A:94 , THR A:120 , ARG A:172 , ILE A:198 , PHE A:261 , ILE A:265 , HIS A:268 , LEU A:269 , PHE A:276 , HOH A:318BINDING SITE FOR RESIDUE ELA A 301
2AC2SOFTWAREVAL A:25 , LEU A:26 , ASP A:27 , GLU A:68BINDING SITE FOR RESIDUE GOL A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LUP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LUP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LUP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LUP)

(-) Exons   (0, 0)

(no "Exon" information available for 3LUP)

(-) 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:283
 aligned with D4AEP8_STRA5 | D4AEP8 from UniProtKB/TrEMBL  Length:285

    Alignment length:283
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
         D4AEP8_STRA5     3 AMKLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPKTSQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKITSAPQGNLVRNALMCSREGMDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIGNLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEIVKEMTADGEYDIAIIHSRAQDKAEQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAVAFGITPKN 285
               SCOP domains d3lupa_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------DegV-3lupA01 A:72-281                                                                                                                                                                                             - Pfam domains
         Sec.struct. author ...eeeeee..............eeee...ee............hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhh....hhhhhhhhhh....eeee.....eeeee...hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lup A   0 AmKLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPKTSQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKITSAPQGNLVRNALmCSREGmDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIGNLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEIVKEmTADGEYDIAIIHSRAQDKAEQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAVAFGITPKN 282
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   |   139       149       159       169       179       189       199       209       219 |     229       239       249       259       269       279   
                             |                                                                                                                                 133-MSE |                                                                               221-MSE                                                         
                             1-MSE                                                                                                                                   139-MSE                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:283
 aligned with Q8DYY0_STRA5 | Q8DYY0 from UniProtKB/TrEMBL  Length:282

    Alignment length:283
                             1                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
         Q8DYY0_STRA5     - -MKLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPKTSQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKITSAPQGNLVRNALMCSREGMDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIGNLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEIVKEMTADGEYDIAIIHSRAQDKAEQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAVAFGITPKN 282
               SCOP domains d3lupa_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------DegV-3lupA01 A:72-281                                                                                                                                                                                             - Pfam domains
         Sec.struct. author ...eeeeee..............eeee...ee............hhhhhhhhhhhh....ee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeee...hhhhhhh....hhhhhhhhhh....eeee.....eeeee...hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lup A   0 AmKLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPKTSQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKITSAPQGNLVRNALmCSREGmDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIGNLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEIVKEmTADGEYDIAIIHSRAQDKAEQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAVAFGITPKN 282
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129   |   139       149       159       169       179       189       199       209       219 |     229       239       249       259       269       279   
                             1-MSE                                                                                                                             133-MSE |                                                                               221-MSE                                                         
                                                                                                                                                                     139-MSE
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LUP)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: EDD (22)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D4AEP8_STRA5 | D4AEP8)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

Chain A   (Q8DYY0_STRA5 | Q8DYY0)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

 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
    ELA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lup)
 

(-) 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
  3lup
    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
  D4AEP8_STRA5 | D4AEP8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q8DYY0_STRA5 | Q8DYY0
    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
  D4AEP8_STRA5 | D4AEP8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8DYY0_STRA5 | Q8DYY0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3LUP)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LUP)