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 A PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (LBUL_1103) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.61 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Jul 08  (Deposition) - 12 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Plp-Dependent Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Pyridoxal 5'-Phosphate-Dependent C-S Lyase (Yp_813084. 1) From Lactobacillus Delbrueckii Bulgaricus Atcc Baa-365 At 1. 61 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PYRIDOXAL 5'-PHOSPHATE-DEPENDENT C-S LYASE
    Atcc: BAA-365
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_813084.1, LBUL_1103
    Organism Scientific: LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS ATCC BAA-365
    Organism Taxid: 321956
    Synonym: BIFUNCTIONAL PLP-DEPENDENT ENZYME WITH BETA-CYSTATHIONASE AND MALTOSE REGULON REPRESSOR ACTIVITIES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 34)

Asymmetric/Biological Unit (7, 34)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5MSE20Mod. Amino AcidSELENOMETHIONINE
6PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
7PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:208 , HOH A:594 , HOH A:595 , HOH A:617 , ASP B:150 , GLU B:153BINDING SITE FOR RESIDUE CA A 391
02AC2SOFTWAREGLU A:308 , HOH A:555 , HOH A:561BINDING SITE FOR RESIDUE CA A 392
03AC3SOFTWAREARG A:255BINDING SITE FOR RESIDUE CL A 393
04AC4SOFTWAREILE A:33 , ALA A:34 , TYR A:118 , LLP A:233 , ARG A:364 , HOH A:514 , HOH A:516 , HOH A:612 , TYR B:59BINDING SITE FOR RESIDUE ACT A 394
05AC5SOFTWAREARG B:255BINDING SITE FOR RESIDUE CL B 391
06AC6SOFTWARETYR A:59 , ILE B:33 , ALA B:34 , TYR B:118 , LLP B:233 , ARG B:364 , HOH B:557 , HOH B:595 , HOH B:597BINDING SITE FOR RESIDUE ACT B 392
07AC7SOFTWAREALA B:189 , GLN B:192 , ASN B:223 , TRP B:224 , ASN B:249 , HOH B:514BINDING SITE FOR RESIDUE PG4 B 393
08AC8SOFTWAREGLN A:192 , ASN A:223 , TRP A:224 , ASN A:249 , HOH A:553BINDING SITE FOR RESIDUE PEG A 395
09AC9SOFTWAREGLN A:15 , HOH A:669BINDING SITE FOR RESIDUE PEG A 396
10BC1SOFTWARELEU A:206 , THR A:207 , ASP A:208 , ARG A:295 , ARG A:302 , HOH A:513 , HOH A:588 , ALA B:149 , GLU B:152 , GLU B:153 , HOH B:559BINDING SITE FOR RESIDUE PEG A 397
11BC2SOFTWARESER A:91 , GLY A:92 , VAL A:94 , PRO A:95 , LLP A:233 , HIS A:241 , GLU B:267 , HOH B:491 , HOH B:579 , HOH B:592BINDING SITE FOR RESIDUE PEG B 394
12BC3SOFTWARETYR B:67 , CYS B:87 , GLU B:257 , HOH B:405 , HOH B:523 , HOH B:548 , HOH B:617BINDING SITE FOR RESIDUE PEG B 395

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Glu A:115 -Pro A:116
2Asn A:167 -Pro A:168
3Asn A:170 -Pro A:171
4Glu B:115 -Pro B:116
5Asn B:167 -Pro B:168
6Asn B:170 -Pro B:171
7Trp B:219 -Asp B:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DZZ)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d3dzza_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................ee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee....hhhhhhhhhhh..eeee...eee..eee.hhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhh...hhh.eeeee.hhhhhh......eeee..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhhhhee.ee.hhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dzz A   4 KQYDFTHVPKRQGNSIKWGVLKEKELPmWIAEmDFKIAPEImASmEEKLKVAAFGYESVPAEYYKAVADWEEIEHRARPKEDWCVFASGVVPAISAmVRQFTSPGDQILVQEPVYNmFYSVIEGNGRRVISSDLIYENSKYSVNWADLEEKLATPSVRmmVFCNPHNPIGYAWSEEEVKRIAELCAKHQVLLISDEIHGDLVLTDEDITPAFTVDWDAKNWVVSLISPSkTFNLAALHAACAIIPNPDLRARAEESFFLAGIGEPNLLAIPAAIAAYEEGHDWLRELKQVLRDNFAYAREFLAKEVPEVKVLDSNASYLAWVDISALGmNAEDFCKYLREKTGLIISAGNGYRGNGHEFVRINLACPKELVIDGmQRLKQGVLNLN 389
                                    13        23       |33  |     43 |  |   53        63        73        83        93      |103       113      |123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    |  383      
                                                      31-MSE|       45-MSE                                                100-MSE             120-MSE                                   162-MSE                                                                233-LLP                                                                                            332-MSE                                       378-MSE       
                                                           36-MSE      48-MSE                                                                                                            163-MSE                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d3dzzb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................ee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhh...eeee...eee..eee.hhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh..eeeee..hhhhh.......hhhhh..hhhh.eeeeehhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhhhhee.ee.hhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dzz B   4 KQYDFTHVPKRQGNSIKWGVLKEKELPmWIAEmDFKIAPEImASmEEKLKVAAFGYESVPAEYYKAVADWEEIEHRARPKEDWCVFASGVVPAISAmVRQFTSPGDQILVQEPVYNmFYSVIEGNGRRVISSDLIYENSKYSVNWADLEEKLATPSVRmmVFCNPHNPIGYAWSEEEVKRIAELCAKHQVLLISDEIHGDLVLTDEDITPAFTVDWDAKNWVVSLISPSkTFNLAALHAACAIIPNPDLRARAEESFFLAGIGEPNLLAIPAAIAAYEEGHDWLRELKQVLRDNFAYAREFLAKEVPEVKVLDSNASYLAWVDISALGmNAEDFCKYLREKTGLIISAGNGYRGNGHEFVRINLACPKELVIDGmQRLKQGVLNL 388
                                    13        23       |33  |     43 |  |   53        63        73        83        93      |103       113      |123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    |  383     
                                                      31-MSE|       45-MSE                                                100-MSE             120-MSE                                   162-MSE                                                                233-LLP                                                                                            332-MSE                                       378-MSE      
                                                           36-MSE      48-MSE                                                                                                            163-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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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 ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:167 - Pro A:168   [ RasMol ]  
    Asn A:170 - Pro A:171   [ RasMol ]  
    Asn B:167 - Pro B:168   [ RasMol ]  
    Asn B:170 - Pro B:171   [ RasMol ]  
    Glu A:115 - Pro A:116   [ RasMol ]  
    Glu B:115 - Pro B:116   [ RasMol ]  
    Trp B:219 - Asp B:220   [ 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
  3dzz
    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 3DZZ)

(-) Related Entries Specified in the PDB File

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