Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  INITIAL STUCTURAL ANALYSIS OF LEISHMANIA MAJOR THREONINE ALDOLASE
 
Authors :  W. G. J. Hol, M. A. Robien, Structural Genomics Of Pathogenic Proto Consortium (Sgpp)
Date :  30 Mar 04  (Deposition) - 17 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Structural Genomics Of Pathogenic Protozoa, Sgpp, Protein Structure Initiative, Psi, Structural Genomics Of Pathogenic Protozoa Consortium, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. G. J. Hol, M. A. Robien, Structural Genomics Of Pathogenic Protozoa
Initial Structural Analysis Of Leishmania Major Threonine Aldolase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THREONINE ALDOLASE
    Chains: A, B
    EC Number: 4.1.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR/DE3
    Expression System Taxid: 562
    Expression System Vector Type: T7 SYSTEM
    Gene: L4171.5
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 52)
No.NameCountTypeFull Name
1MSE48Mod. Amino AcidSELENOMETHIONINE
2UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:37 , HIS A:42 , HIS A:50BINDING SITE FOR RESIDUE UNL A 401
2AC2SOFTWAREASP B:37 , HIS B:42 , HIS B:50BINDING SITE FOR RESIDUE UNL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SVV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:153 -Thr A:154
2Asn B:153 -Thr B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SVV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SVV)

(-) Exons   (0, 0)

(no "Exon" information available for 1SVV)

(-) 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:340
 aligned with E9AC39_LEIMA | E9AC39 from UniProtKB/TrEMBL  Length:359

    Alignment length:340
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354
         E9AC39_LEIMA    15 PYSFVNDYSVGMHPKILDLMARDNMTQHAGYGQDSHCAKAARLIGELLERPDADVHFISGGTQTNLIACSLALRPWEAVIATQLGHISTHETGAIEATGHKVVTAPCPDGKLRVADIESALHENRSEHMVIPKLVYISNTTEVGTQYTKQELEDISASCKEHGLYLFLDGARLASALSSPVNDLTLADIARLTDMFYIGATKAGGMFGEALIILNDALKPNARHLIKQRGALMAKGWLLGIQFEVLMKDNLFFELGAHSNKMAAILKAGLEACGIRLAWPSASNQLFPILENTMIAELNNDFDMYTVEPLKDGTCIMRLCTSWATEEKECHRFVEVLKRL 354
               SCOP domains d1svva_ A: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1svvA01 A:15-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                      1svvA02 A:265-354 Aspartate Aminotransferase, domain 1                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh...eeeeee..hhhhhh..hhhhhh...eeee.......hhhhhhhhhhhh......eeeeeeee.........hhhhhhhhhhhhhhh..eeeee..hhhhhhh......hhhhhhhhh.eeeee.........eeeee.hhhhh.hhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...........ee..eeehhhhhhhh..ee.eeeeee...eeeeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svv A  15 PYSFVNDYSVGmHPKILDLmARDNmTQHAGYGQDSHCAKAARLIGELLERPDADVHFISGGTQTNLIACSLALRPWEAVIATQLGHISTHETGAIEATGHKVVTAPCPDGKLRVADIESALHENRSEHmVIPKLVYISNTTEVGTQYTKQELEDISASCKEHGLYLFLDGARLASALSSPVNDLTLADIARLTDmFYIGATKAGGmFGEALIILNDALKPNARHLIKQRGALmAKGWLLGIQFEVLmKDNLFFELGAHSNKmAAILKAGLEACGIRLAWPSASNQLFPILENTmIAELNNDFDmYTVEPLKDGTCImRLCTSWATEEKECHRFVEVLKRL 354
                                    24 |      34    |   44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    |  214     | 224       234       244  |    254      |264       274 |     284       294       304   |   314   |   324      |334       344       354
                                      26-MSE  34-MSE|                                                                                                     143-MSE                                                           209-MSE    220-MSE                    247-MSE       261-MSE        276-MSE                         308-MSE   318-MSE      331-MSE                   
                                                   39-MSE                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with E9AC39_LEIMA | E9AC39 from UniProtKB/TrEMBL  Length:359

    Alignment length:342
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  
         E9AC39_LEIMA    15 PYSFVNDYSVGMHPKILDLMARDNMTQHAGYGQDSHCAKAARLIGELLERPDADVHFISGGTQTNLIACSLALRPWEAVIATQLGHISTHETGAIEATGHKVVTAPCPDGKLRVADIESALHENRSEHMVIPKLVYISNTTEVGTQYTKQELEDISASCKEHGLYLFLDGARLASALSSPVNDLTLADIARLTDMFYIGATKAGGMFGEALIILNDALKPNARHLIKQRGALMAKGWLLGIQFEVLMKDNLFFELGAHSNKMAAILKAGLEACGIRLAWPSASNQLFPILENTMIAELNNDFDMYTVEPLKDGTCIMRLCTSWATEEKECHRFVEVLKRLVA 356
               SCOP domains d1svvb_ B: Low-specificity threonine aldolase                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1svvB01 B:15-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                      1svvB02 B:265-356 Aspartate Aminotransferase, domain 1                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh...eeeeee..hhhhhh..hhhhhh...eeee.......hhhhhhhhhhhh......eeeeeeee.........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.....hhhhhhhhh.eeeee.........eeeee.hhhhh.hhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...........ee..eeehhhhhhhh..ee.eeeee....eeeeeee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1svv B  15 PYSFVNDYSVGmHPKILDLmARDNmTQHAGYGQDSHCAKAARLIGELLERPDADVHFISGGTQTNLIACSLALRPWEAVIATQLGHISTHETGAIEATGHKVVTAPCPDGKLRVADIESALHENRSEHmVIPKLVYISNTTEVGTQYTKQELEDISASCKEHGLYLFLDGARLASALSSPVNDLTLADIARLTDmFYIGATKAGGmFGEALIILNDALKPNARHLIKQRGALmAKGWLLGIQFEVLmKDNLFFELGAHSNKmAAILKAGLEACGIRLAWPSASNQLFPILENTmIAELNNDFDmYTVEPLKDGTCImRLCTSWATEEKECHRFVEVLKRLVA 356
                                    24 |      34    |   44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    |  214     | 224       234       244  |    254      |264       274 |     284       294       304   |   314   |   324      |334       344       354  
                                      26-MSE  34-MSE|                                                                                                     143-MSE                                                           209-MSE    220-MSE                    247-MSE       261-MSE        276-MSE                         308-MSE   318-MSE      331-MSE                     
                                                   39-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SVV)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E9AC39_LEIMA | E9AC39)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:153 - Thr A:154   [ RasMol ]  
    Asn B:153 - Thr B:154   [ RasMol ]  
 
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
  1svv
    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
  E9AC39_LEIMA | E9AC39
    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)
  4.1.2.5
    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
  E9AC39_LEIMA | E9AC39
    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 1SVV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SVV)