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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE CARBOXYPEPTIDASE (YP_103406.1) FROM BURKHOLDERIA MALLEI ATCC 23344 AT 2.49 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Sep 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Putative Carboxypeptidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Carboxypeptidase (Yp_103406. 1 From Burkholderia Mallei Atcc 23344 At 2. 49 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE CARBOXYPEPTIDASE
    Atcc: 23344
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BMA1798
    Organism Common: PSEUDOMONAS MALLEI
    Organism Scientific: BURKHOLDERIA MALLEI ATCC 23344
    Organism Taxid: 243160

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MSE44Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:303 , GLN A:310 , ASP A:311BINDING SITE FOR RESIDUE CL A 385
2AC2SOFTWARESER A:7 , ALA A:13 , ILE A:14 , ARG A:30BINDING SITE FOR RESIDUE CL A 386
3AC3SOFTWAREHIS A:171 , ARG A:226 , ASN A:235 , ARG A:236BINDING SITE FOR RESIDUE CL A 387
4AC4SOFTWAREARG A:335 , HOH A:464BINDING SITE FOR RESIDUE CL A 388
5AC5SOFTWAREARG A:44 , SER A:105 , HIS A:119 , SER A:120 , SER A:147 , HOH A:473 , HOH A:484BINDING SITE FOR RESIDUE GOL A 389

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K2K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2K)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2K)

(-) 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:387
 aligned with A0A0H2WJQ2_B | A0A0H2WJQ2 from UniProtKB/TrEMBL  Length:384

    Alignment length:391
                                    1                                                                                                                                                                                                                                                                                                                                                                                              
                                    |2        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       292       302       312       322       332       342       352       362       372       382 
         A0A0H2WJQ2_B     - --------MTLSITSNFDAGAIDVVSCERADAIRLRVRGDNRSEFAQWFYFRLTGARGERCVMTFENANDCAYPAGWRDYRAVASYDRVNWFRVPTSYDGQMLTIDHTPEFDSIHYAYFEPYSEERHSEFLGAVQQMPQASVVELGRTVEGRPMSLVVLGTPDEAGAAKKKVWIIARQHPGESMAEWFIEGLVKRLVGWGDWSGDPVARKLYDHATFYIVPNMNPDGSVHGNLRTNAAGANLNREWMEPDAERSPEVLVVRDAIHAIGCDLFFDIHGDEDLPYVFAAGSEMLPGFTEQQRVEQSAFIDSFKRASPDFQDEHGYPPGKYREDAFKLASKYIGHRFGCLSLTLEMPFKDNANLPDEHIGWNGARSASLGAAMLGAILEHVRAF 383
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee........eeee..hhhheeee.............eeeee......eeeee.hhhhh.hhhhhh....eee......ee..eee....eeeee.....eeeee.....hhhhhhhhhhhhh....eeeeeeee.....eeeeeee....----..eeeeeee......hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhheeeeee...hhhhhhh..........hhhhh........hhhhhhhhhhhhhhh..eeeeeeee......eee........hhhhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhh.eeeeeeee..............hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2k A  -7 HENLYFQGmTLSITSNFDAGAIDVVSCERADAIRLRVRGDNRSEFAQWFYFRLTGARGERCVmTFENANDCAYPAGWRDYRAVASYDRVNWFRVPTSYDGQmLTIDHTPEFDSIHYAYFEPYSEERHSEFLGAVQQmPQASVVELGRTVEGRPmSLVVLGTPD----AKKKVWIIARQHPGESmAEWFIEGLVKRLVGWGDWSGDPVARKLYDHATFYIVPNmNPDGSVHGNLRTNAAGANLNREWmEPDAERSPEVLVVRDAIHAIGCDLFFDIHGDEDLPYVFAAGSEmLPGFTEQQRVEQSAFIDSFKRASPDFQDEHGYPPGKYREDAFKLASKYIGHRFGCLSLTLEmPFKDNANLPDEHIGWNGARSASLGAAmLGAILEHVRAF 383
                                    |2        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|      292       302       312       322       332       342  |    352       362       372       382 
                                    1-MSE                                                55-MSE                                 94-MSE                            129-MSE          146-MSE  155  160             176-MSE                                215-MSE                 239-MSE                                     283-MSE                                                       345-MSE                    372-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 3K2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K2K)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3K2K)

 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
    CL  [ 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 ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3k2k)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  3k2k
    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
  A0A0H2WJQ2_B | A0A0H2WJQ2
    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
  A0A0H2WJQ2_B | A0A0H2WJQ2
    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 3K2K)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K2K)