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 ACYLAMINOACYL PEPTIDASE SMU_737 FROM STREPTOCOCCUS MUTANS UA159
 
Authors :  Y. Kim, C. Hatzos, G. Cobb, A. Joachimiak, Midwest Center For Struct Genomics (Mcsg)
Date :  23 Dec 08  (Deposition) - 06 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta-Alpha Sandwich, Helix Bundle, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Hatzos, G. Cobb, A. Joachimiak
Crystal Structure Of Acylaminoacyl-Peptidase Smu_737 From Streptococcus Mutans Ua159
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYLAMINOACYL PEPTIDASE SMU_737
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMU_737
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 210007
    Strain: UA159

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 28)

Asymmetric/Biological Unit (5, 28)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4MSE20Mod. Amino AcidSELENOMETHIONINE
5PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:366 , LYS A:367 , PHE A:368 , SER A:369 , HOH B:522BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP A:166 , MSE A:175 , HIS A:377 , CYS A:378 , HOH A:500BINDING SITE FOR RESIDUE BME A 403
3AC3SOFTWAREPHE A:238 , HOH A:538BINDING SITE FOR RESIDUE PGE A 404
4AC4SOFTWARETYR A:45 , ILE A:46 , SER A:48 , GLY A:49 , ARG A:61BINDING SITE FOR RESIDUE EDO A 405
5AC5SOFTWARETYR A:68 , HOH A:510 , ARG B:366 , LYS B:367 , SER B:369BINDING SITE FOR RESIDUE MG B 501
6AC6SOFTWAREHIS B:377 , CYS B:378BINDING SITE FOR RESIDUE BME B 403
7AC7SOFTWAREGLU B:206 , PHE B:238 , EDO B:405BINDING SITE FOR RESIDUE PGE B 404
8AC8SOFTWAREPGE B:404 , HOH B:489BINDING SITE FOR RESIDUE EDO B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:255 -Thr A:256
2Ser B:255 -Thr B:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FNB)

(-) 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:374
 aligned with Q8DUZ1_STRMU | Q8DUZ1 from UniProtKB/TrEMBL  Length:402

    Alignment length:392
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397  
         Q8DUZ1_STRMU     8 LKRQDYKIKFNNKDMDFCFNWMLGIGQIIGMSAGELFYIASGIRDGNPTDWCKRFNEHADYLEDEVERVKKVGYRDLISHLYFSACFSIRAALQFTDPKDSEFMENFRRMEKLFMLAVDNSKIPLKSIEVPFEGELLPGYAIISEDKAQDTLIVVGGGDTSREDLFYMLGYSGWEHDYNVLMVDLPGQGKNPNQGLHFEVDARAAISAILDWYQAPTEKIAIAGFSGGGYFTAQAVEKDKRIKAWIASTPIYDVAEVFRISFSTALKAPKTILKWGSKLVTSVNKVAEVNLNKYAWQFGQVDFITSVNEVLEQAQIVDYNKIDVPSLFLVGAGEDSELMRQSQVLYDNFKQRGIDVTLRKFSSESGADAHCQVNNFRLMHYQVFEWLNHIFK 399
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------3fnbA02 A:133-399  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee........eeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......hhhhhhhhhhhh......eeeeee.hhhhhhhhhhh......eeeee....hhhhhhhhhh.------------------..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhh...eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fnb A   8 LKRQDYKIKFNNKDmDFCFNWmLGIGQIIGmSAGELFYIASGIRDGNPTDWCKRFNEHADYLEDEVERVKKVGYRDLISHLYFSACFSIRAALQFTDPKDSEFmENFRRmEKLFmLAVDNSKIPLKSIEVPFEGELLPGYAIISEDKAQDTLIVVGGGDTSREDLFYmLGYSGWEHDYNVLmVDLPGQGKNPNQGLHFEVDARAAISAILDWYQAPTEKIAIAGFSGGGYFTAQAVEKDKRIKAWIASTPIYDVAEVFRISFS------------------SVNKVAEVNLNKYAWQFGQVDFITSVNEVLEQAQIVDYNKIDVPSLFLVGAGEDSELmRQSQVLYDNFKQRGIDVTLRKFSSESGADAHCQVNNFRLmHYQVFEWLNHIFK 399
                                    17    |   27 |      37|       47        57        67        77        87        97       107   |   117    |  127       137       147       157       167       177       187 |     197       207       217       227       237       247       257       267  |      -         - |     297       307       317       327       337       347       357       367       377       387       397  
                                         22-MSE 29-MSE   38-MSE                                                                  111-MSE |    |                                                  175-MSE       189-MSE                                                                          270                289                                                      346-MSE                                 386-MSE         
                                                                                                                                       117-MSE|                                                                                                                                                                                                                                                                                     
                                                                                                                                            122-MSE                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with Q8DUZ1_STRMU | Q8DUZ1 from UniProtKB/TrEMBL  Length:402

    Alignment length:390
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
         Q8DUZ1_STRMU    11 QDYKIKFNNKDMDFCFNWMLGIGQIIGMSAGELFYIASGIRDGNPTDWCKRFNEHADYLEDEVERVKKVGYRDLISHLYFSACFSIRAALQFTDPKDSEFMENFRRMEKLFMLAVDNSKIPLKSIEVPFEGELLPGYAIISEDKAQDTLIVVGGGDTSREDLFYMLGYSGWEHDYNVLMVDLPGQGKNPNQGLHFEVDARAAISAILDWYQAPTEKIAIAGFSGGGYFTAQAVEKDKRIKAWIASTPIYDVAEVFRISFSTALKAPKTILKWGSKLVTSVNKVAEVNLNKYAWQFGQVDFITSVNEVLEQAQIVDYNKIDVPSLFLVGAGEDSELMRQSQVLYDNFKQRGIDVTLRKFSSESGADAHCQVNNFRLMHYQVFEWLNHIFKK 400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------3fnbB02 B:133-400  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeee........eeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......hhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhhhhhh.-------------------.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhh...eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fnb B  11 QDYKIKFNNKDmDFCFNWmLGIGQIIGmSAGELFYIASGIRDGNPTDWCKRFNEHADYLEDEVERVKKVGYRDLISHLYFSACFSIRAALQFTDPKDSEFmENFRRmEKLFmLAVDNSKIPLKSIEVPFEGELLPGYAIISEDKAQDTLIVVGGGDTSREDLFYmLGYSGWEHDYNVLmVDLPGQGKNPNQGLHFEVDARAAISAILDWYQAPTEKIAIAGFSGGGYFTAQAVEKDKRIKAWIASTPIYDVAEVFRISFS-------------------VNKVAEVNLNKYAWQFGQVDFITSVNEVLEQAQIVDYNKIDVPSLFLVGAGEDSELmRQSQVLYDNFKQRGIDVTLRKFSSESGADAHCQVNNFRLmHYQVFEWLNHIFKK 400
                                    20 |      30       |40        50        60        70        80        90       100       110|     |120 |     130       140       150       160       170    |  180       190       200       210       220       230       240       250       260       270         -       290       300       310       320       330       340     | 350       360       370       380     | 390       400
                                      22-MSE 29-MSE   38-MSE                                                                  111-MSE |    |                                                  175-MSE       189-MSE                                                                          270                 290                                                     346-MSE                                 386-MSE          
                                                                                                                                    117-MSE|                                                                                                                                                                                                                                                                                      
                                                                                                                                         122-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 3FNB)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FNB)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8DUZ1_STRMU | Q8DUZ1)
molecular function
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
 
  Cis Peptide Bonds
    Ser A:255 - Thr A:256   [ RasMol ]  
    Ser B:255 - Thr B:256   [ 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 | 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
  3fnb
    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
  Q8DUZ1_STRMU | Q8DUZ1
    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
  Q8DUZ1_STRMU | Q8DUZ1
    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 3FNB)

(-) Related Entries Specified in the PDB File

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