Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN KYNURENINE AMINOTRANSFERASE-I BOUND TO PLP COFACTOR
 
Authors :  N. A. Nadvi, N. K. Salam, J. Park, F. N. Akladios, V. Kapoor, C. A. Collyer M. D. Gorrell, W. B. Church
Date :  07 Oct 14  (Deposition) - 03 Dec 14  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Alternate Conformations, Alpha Beta Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. A. Nadvi, N. K. Salam, J. Park, F. N. Akladios, V. Kapoor, C. A. Collyer, M. D. Gorrell, W. B. Church
High Resolution Crystal Structures Of Human Kynurenine Aminotransferase-I Bound To Plp Cofactor, And In Complex With Aminooxyacetate.
Protein Sci. V. 26 727 2017
PubMed-ID: 28097769  |  Reference-DOI: 10.1002/PRO.3119

(-) Compounds

Molecule 1 - KYNURENINE--OXOGLUTARATE TRANSAMINASE 1
    Chains: A, B
    EC Number: 2.6.1.7, 4.4.1.13, 2.6.1.64
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PBLUEBAC4.5
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: KYAT1, CCBL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYSTEINE-S-CONJUGATE BETA-LYASE,GLUTAMINE TRANSAMINASE K, GTK,GLUTAMINE--PHENYLPYRUVATE TRANSAMINASE,KYNURENINE AMINOTRANSFERASE 1,KYNURENINE AMINOTRANSFERASE I,KATI,KYNURENINE-- OXOGLUTARATE TRANSAMINASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4WLH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:122 -Pro A:123
2Thr A:182 -Pro A:183
3Asn A:185 -Pro A:186
4Glu B:122 -Pro B:123
5Thr B:182 -Pro B:183
6Asn B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WLH)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....hhhhhhhhhhh...ee..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee......hhhhh..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh..hhh.eeeeeehhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeehhhhhhhh.........hhhhhhhhhhhhhhhee.ee.hhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlh A   4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGkTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  ||   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419   
                                                                                                                                                                        146|                                                                                           247-LLP                                                                                                                                                                           
                                                                                                                                                                         153                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh......hhhhhhhhhhh..ee..........hhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh...hhhhheeeehhhhhhhhhhhhhhh....eeeeee....hhhhhhhhh..eeeeee.....hhhhh..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhh..hhh.eeeeeehhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeehhhhhhhh.........hhhhhhhhhhhhhhhee.ee.hhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlh B   4 QLQARRLDGIDYNPWVEFVKLASEHDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPLGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHDVVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGkTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQSVGLKPIIPQGSYFLITDISDFKRKMPDLPGAVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRKWKVEL 422
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  ||   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       410       420  
                                                                                                                                                                        146|                                                                                          247-LLP                                                                                                                                                                           
                                                                                                                                                                         154
   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 4WLH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WLH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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
    LLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4wlh)
 
  Cis Peptide Bonds
    Asn A:185 - Pro A:186   [ RasMol ]  
    Asn B:185 - Pro B:186   [ RasMol ]  
    Glu A:122 - Pro A:123   [ RasMol ]  
    Glu B:122 - Pro B:123   [ RasMol ]  
    Thr A:182 - Pro A:183   [ RasMol ]  
    Thr B:182 - Pro B:183   [ 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 ](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
  4wlh
    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
  KAT1_HUMAN | Q16773
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.64
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.6.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  4.4.1.13
    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
  KAT1_HUMAN | Q16773
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KAT1_HUMAN | Q16773: 1w7l 1w7m 1w7n 3fvs 3fvu 3fvx 4wlj 4wp0

(-) Related Entries Specified in the PDB File

4wlj