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 :  APO CRYSTAL STRUCTURE OF PYRUVATE KINASE (PYK) FROM TRYPANOSOMA CRUZI
 
Authors :  W. Zhong, H. P. Morgan, I. W. Mcnae, P. A. M. Michels, L. A. Fothergill-Gi M. D. Walkinshaw
Date :  17 May 13  (Deposition) - 19 Nov 14  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tetramer, Pyruvate Kinase, Allostery, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Morgan, W. Zhong, I. W. Mcnae, P. A. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
Structures Of Pyruvate Kinases Display Evolutionarily Divergent Allosteric Strategies.
R Soc Open Sci V. 1 40120 2014
PubMed-ID: 26064527  |  Reference-DOI: 10.1098/RSOS.140120

(-) Compounds

Molecule 1 - PYRUVATE KINASE
    Chains: A, B
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TC00.1047053511281.60
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 353153
    Strain: CL BRENER

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:52 , SER A:54 , ASP A:84 , THR A:85 , LYS A:239 , GOL A:502 , HOH A:813BINDING SITE FOR RESIDUE K A 501
2AC2SOFTWARESER A:54 , THR A:85 , LYS A:86 , SER A:212 , GLU A:241 , ASP A:265 , K A:501BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREARG B:50 , ASN B:52 , SER B:54 , ASP B:84 , THR B:85BINDING SITE FOR RESIDUE K B 501
4AC4SOFTWAREGLU B:89 , ILE B:90 , CYS B:178 , ASN B:179 , HOH B:685BINDING SITE FOR RESIDUE GOL B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:373 -Pro A:374
2Leu B:373 -Pro B:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KRZ)

(-) 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:494
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee..........hhh.eeee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee....eeeeee...eeee....ee...........hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krz A   1 MSQLAHNVNLSIFEPISHHRANRIVCTIGPSTQSVEALKGLIRSGMSVARMNFSHGSHEYHQTTINNLRAAATELGAHIGLALDTKGPEIRTGLFKDGGIALAPGDTVLVTSDPAFEKIGTKEKFYIEYPRLSITVRPGGFIYIDDGVLSLKVLSKEDEYTLKCYVNNAHFLTDRKGCNLPGCEVDLPAVSEKDREDLKFGVEQGIDMVFASFIRTAEQVQEVREALGEKGKDILIISKIENHQGVQNIDGIIEASDGIMVARGDLGVEIPAEKVVVAQMILISKCNVAGKPVICATQMLESMTTNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSATNQAVMFNSIKKMQKLPMSPEEAVCSSAVNSVYEVRAKALLVLSNSGRSARLASKYRPDCPIICATTRMRTCRQLTITRSVDAVFYDAERYGEDENKEKRVQLGVDCAKKKGYVVPGDLMVVVHADHPNQTRIIYVS 499
                                    10        20        30        40        50        60        70        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       370       380       390       400       410       420       430       440       450       460       470       480   ||  495    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             484|         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              490         


Chain B from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.............eeeee......hhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhhhh....eeeee..........hhh.eeee....eeeee............eee....hhhhhh....eeee....eeeeeeee....eeeeee...eeee....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krz B   1 MSQLAHNVNLSIFEPISHHRANRIVCTIGPSTQSVEALKGLIRSGMSVARMNFSHGSHEYHQTTINNLRAAATELGAHIGLALDTKGPEIRTGLFKDGGIALAPGDTVLVTSDPAFEKIGTKEKFYIEYPRLSITVRPGGFIYIDDGVLSLKVLSKEDEYTLKCYVNNAHFLTDRKGCNLPGCEVDLPAVSEKDREDLKFGVEQGIDMVFASFIRTAEQVQEVREALGEKGKDILIISKIENHQGVQNIDGIIEASDGIMVARGDLGVEIPAEKVVVAQMILISKCNVAGKPVICATQMLESMTTNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSATNQAVMFNSIKKMQKLPMSPEEAVCSSAVNSVYEVRAKALLVLSNSGRSARLASKYRPDCPIICATTRMRTCRQLTITRSVDAVFYDAERYGEDENKEKRVQLGVDCAKKKGYVVPGDLMVVVHADGYPNQTRIIYVS 499
                                    10        20        30        40        50        60        70        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       370       380       390       400       410       420       430       440       450       460       470       480  ||   494     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            483|           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             488
   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 4KRZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:373 - Pro A:374   [ RasMol ]  
    Leu B:373 - Pro B:374   [ 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
  4krz
    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
  Q4D9Z4_TRYCC | Q4D9Z4
    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)
  2.7.1.40
    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
  Q4D9Z4_TRYCC | Q4D9Z4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4D9Z4_TRYCC | Q4D9Z4: 3qv9 4ks0

(-) Related Entries Specified in the PDB File

3qv9 CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI PYRUVATE KINASE(TCPYK)IN COMPLEX WITH PONCEAU S.
4ks0