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 TYROSINE AMINOTRANSFERASE FROM LEISHMANIA INFANTUM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  24 Jan 13  (Deposition) - 26 Mar 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Tyrosine Aminotransferase, Pyridoxal Phosphate, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Moreno, A. Abramov, J. Abendroth, A. Alonso, S. Zhang, P. J. Alcolea, T. Edwards, D. Lorimer, P. J. Myler, V. Larraga
Structure Of Tyrosine Aminotransferase From Leishmania Infantum.
Acta Crystallogr F Struct V. 70 583 2014 Biol Commun
PubMed-ID: 24817714  |  Reference-DOI: 10.1107/S2053230X14007845

(-) Compounds

Molecule 1 - TYROSINE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: LEINA.00674.A.BV2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LEINA.00674.A.BV2
    Gene: LINJ_36_2490, TAT
    Organism Scientific: LEISHMANIA INFANTUM
    Organism Taxid: 5671

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:778BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWAREGLN B:152BINDING SITE FOR RESIDUE CL B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IX8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:172 -Pro A:173
2Asn A:222 -Pro A:223
3Asn A:225 -Pro A:226
4Ala B:172 -Pro B:173
5Asn B:222 -Pro B:223
6Asn B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IX8)

(-) Exons   (0, 0)

(no "Exon" information available for 4IX8)

(-) 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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ix8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..hhhhhhh..........ee..............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhh.hhh.eeeehhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.eeeeee.........hhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhhh..eeee........................eeeeee......hhhhh.eeeeee.....hhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...ee........eeeeee.hhhh....hhhhhhhhhhhhhhee.ee.hhhh...eeeee...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ix8 A  40 SFRRIASSKHAQRTLQPLNNLTMKPSRSTKSNLRLSIGDPTVDGNLKTPDIVTEAMVDVVRSGKFNGYPPTVGADNLRQVVSTYWRRFCQTKSRQEALKWENVIITSGVSQAIVLALTALCNEGDNILVCAPSFPHYKSVCDSYGIECRYYYLDPSKSWECDLRAAAGMVDSHTKAFVIINPSNPCGSNFSRAHVSDIIDFCQQHQIPLISDEIYAEMVLNNGIFTSVADFDTNVPRLILGGTAkYQVCPGWRVGWSILIDPMNVAGDWAVGMERLTQLIAGVNSICQEAIARTLLKCPTECTEHIVTQLEAGAKVYARLLEHDIGISMEAPQASMFVMLKLNLSYFQDLKSDMEFYEKLLDEENVQVLPGEIFGMSGFLRATVSRPSAVLNEAVDRIIEFCERHKK 448
                                    49        59 ||     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    |  291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       
                                                61|                                                                                                                                                                                                                           286-LLP                                                                                                                                                              
                                                 64                                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4ix8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..hhhhhhh.ee..............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhh.eeeehhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.eeeeee.hhhhh...hhhhhhh.....eeeeeee..........hhhhhhhhhhhhhhhh..eeee........................eeeee.......hhhhh.eeeeee.....hhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh............eeee.hhhhhhhhh.ee.ee.hhhh....eeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ix8 B  40 SFRRIASSKHAQRTLQPLNNLTNLRLSIGDPTVDGNLKTPDIVTEAMVDVVRSGKFNGYPPTVGADNLRQVVSTYWRRFCQTKSRQEALKWENVIITSGVSQAIVLALTALCNEGDNILVCAPSFPHYKSVCDSYGIECRYYYLDPSKSWECDLRAAAGMVDSHTKAFVIINPSNPCGSNFSRAHVSDIIDFCQQHQIPLISDEIYAEMVLNNGIFTSVADFDTNVPRLILGGTAkYQVCPGWRVGWSILIDPMNVAGDWAVGMERLTQLIAGVNSICQEAIARTLLKCPTECTEHIVTQLEAGAKVYARLLISMEAPQASMFVMLDMEFYEKLLDNVQVLPGEIFGMSGFLRATVSRPSAVLNEAVDRI 439
                                    49        59 ||     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 ||    375     ||397     ||409       419       429       439
                                                61|                                                                                                                                                                                                                  286-LLP                                                                     362|          381|      403|                                 
                                                 73                                                                                                                                                                                                                                                                                               368           394       406
   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 4IX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IX8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:172 - Pro A:173   [ RasMol ]  
    Ala B:172 - Pro B:173   [ RasMol ]  
    Asn A:222 - Pro A:223   [ RasMol ]  
    Asn A:225 - Pro A:226   [ RasMol ]  
    Asn B:222 - Pro B:223   [ RasMol ]  
    Asn B:225 - Pro B:226   [ 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
  4ix8
    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
  A4IDL0_LEIIN | A4IDL0
    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)
  2.6.1.5
    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
  A4IDL0_LEIIN | A4IDL0
    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 4IX8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4IX8)