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

(-) Description

Title :  STRUCTURE OF STRINGENT STARVATION PROTEIN A HOMOLOG FROM PSEUDOMONAS FLUORESCENS
 
Authors :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  28 Feb 10  (Deposition) - 23 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Gst-Superfamily, Sspa, Stringent Starvation Protein A Homolog, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Structure Of Stringent Starvation Protein A Homolog From Pseudomonas Fluorescens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - STRINGENT STARVATION PROTEIN A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: PFL_5077, SSPA
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 220664
    Strain: PF-5 / ATCC BAA-477

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LYP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:57 -Pro A:58
2His A:83 -Pro A:84
3Leu B:57 -Pro B:58
4His B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LYP)

(-) 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:196
 aligned with Q4K6H7_PSEF5 | Q4K6H7 from UniProtKB/TrEMBL  Length:205

    Alignment length:200
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
         Q4K6H7_PSEF5     6 RLACYSDPADHYSHRVRIVLAEKGVSAEIISVEAGRQPPKLIEVNPYGSLPTLVDRDLALWESTVVMEYLDERYPHPPLLPVYPVARANSRLLIHRIQRDWCGQVDLILDPRTKEAARVQARKELRESLTGVSPLFADKPFFLSEEQSLVDCCLLPILWRLPVLGIELPRQAKPLLDYMERQFAREAFQASLSGVERDMR 205
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhh...eeee..---.hhhhhhhh......eee..-.eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lyp A   8 RLACYSDPADHYSHRVRIVLAEKGVSAEIISVE---QPPKLIEVNPYGSLPTLVDR-LALWESTVVmEYLDERYPHPPLLPVYPVARANSRLLIHRIQRDWCGQVDLILDPRTKEAARVQARKELRESLTGVSPLFADKPFFLSEEQSLVDCCLLPILWRLPVLGIELPRQAKPLLDYmERQFAREAFQASLSGVERDmR 207
                                    17        27        37  |   | 47        57     | |67      | 77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                                           40  44                 63 |       74-MSE                                                                                                         186-MSE             206-MSE
                                                                                    65                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Q4K6H7_PSEF5 | Q4K6H7 from UniProtKB/TrEMBL  Length:205

    Alignment length:199
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196         
         Q4K6H7_PSEF5     7 LACYSDPADHYSHRVRIVLAEKGVSAEIISVEAGRQPPKLIEVNPYGSLPTLVDRDLALWESTVVMEYLDERYPHPPLLPVYPVARANSRLLIHRIQRDWCGQVDLILDPRTKEAARVQARKELRESLTGVSPLFADKPFFLSEEQSLVDCCLLPILWRLPVLGIELPRQAKPLLDYMERQFAREAFQASLSGVERDMR 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---GST_N_3-3lypB03 B:12-85                                                   ---------GST_C_2-3lypB01 B:95-188                                                                      ------------------- Pfam domains (1)
           Pfam domains (2) ---GST_N_3-3lypB04 B:12-85                                                   ---------GST_C_2-3lypB02 B:95-188                                                                      ------------------- Pfam domains (2)
         Sec.struct. author .eeee...hhhhhhhhhhhhhhh...eeee....--hhhhhhhh......eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lyp B   9 LACYSDPADHYSHRVRIVLAEKGVSAEIISVEAG--PPKLIEVNPYGSLPTLVDRDLALWESTVVmEYLDERYPHPPLLPVYPVARANSRLLIHRIQRDWCGQVDLILDPRTKEAARVQARKELRESLTGVSPLFADKPFFLSEEQSLVDCCLLPILWRLPVLGIELPRQAKPLLDYmERQFAREAFQASLSGVERDmR 207
                                    18        28        38   |  | 48        58        68     |  78        88        98       108       118       128       138       148       158       168       178       188       198       | 
                                                            42 45                           74-MSE                                                                                                         186-MSE             206-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  (0, 0)

(no "SCOP Domain" information available for 3LYP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LYP)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3lyp)
 
  Cis Peptide Bonds
    His A:83 - Pro A:84   [ RasMol ]  
    His B:83 - Pro B:84   [ RasMol ]  
    Leu A:57 - Pro A:58   [ RasMol ]  
    Leu B:57 - Pro B:58   [ RasMol ]  
 

(-) 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 ](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
  3lyp
    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
  Q4K6H7_PSEF5 | Q4K6H7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q4K6H7_PSEF5 | Q4K6H7
    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 3LYP)

(-) Related Entries Specified in the PDB File

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