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 :  F96S/S73A DOUBLE MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
 
Authors :  V. Pareek, P. Balaram, M. R. N. Murthy
Date :  26 Mar 15  (Deposition) - 03 Feb 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrels, Beta-Alpha Barrels, Isomerase, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Pareek, M. Samanta, N. V. Joshi, H. Balaram, M. R. N. Murthy, P. Balaram
Connecting Active-Site Loop Conformations And Catalysis In Triosephosphate Isomerase: Insights From A Rare Variation A Residue 96 In The Plasmodial Enzyme
Chembiochem V. 17 620 2016
PubMed-ID: 26762569  |  Reference-DOI: 10.1002/CBIC.201500532

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: AA200
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TPI
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Other Details: MUTATION OF A163V PRESENT IN THE WILD TYPE TIM CONSIDERED AS TEMPLATE
    Synonym: TIM,TRIOSE-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:45 , VAL A:46 , TYR A:48 , ASP A:49 , LEU A:86 , HOH A:484 , VAL B:46 , HOH B:404binding site for residue EDO A 301
02AC2SOFTWARELEU A:117 , ASN A:120 , ASN A:159 , HOH A:412binding site for residue EDO A 302
03AC3SOFTWARECYS A:196 , GLY A:197 , HOH A:404 , HOH A:433 , ARG B:52 , LYS B:53 , LEU B:55binding site for residue EDO A 303
04AC4SOFTWAREASN A:71 , GLU A:81 , HOH A:420 , GLY B:15 , THR B:16binding site for residue EDO A 304
05AC5SOFTWAREASN A:65 , ARG A:98 , GLU A:104 , LYS A:112 , HOH A:466 , HOH A:507binding site for residue SO4 A 305
06AC6SOFTWARESER A:211 , GLY A:232 , ASN A:233 , HOH A:424 , HOH A:432 , HOH A:446 , HOH A:451binding site for residue SO4 A 306
07AC7SOFTWAREASN B:137 , ILE B:140 , EDO B:303binding site for residue EDO B 301
08AC8SOFTWAREHIS A:50 , ASP B:49 , HOH B:448binding site for residue EDO B 302
09AC9SOFTWAREASN B:137 , LYS B:138 , ILE B:140 , GLU B:141 , EDO B:301binding site for residue EDO B 303
10AD1SOFTWARESER B:19 , SER B:22 , LEU B:23 , GLU B:238binding site for residue EDO B 304
11AD2SOFTWARELYS B:186 , LYS B:190 , HOH B:417 , HOH B:460binding site for residue EDO B 305
12AD3SOFTWARELEU B:117 , ASN B:120 , LEU B:121 , ASP B:155 , ASN B:156 , ASN B:159binding site for residue EDO B 306
13AD4SOFTWARELYS A:148 , HOH A:428 , SER B:60 , GLU B:89 , HOH B:429binding site for residue EDO B 307
14AD5SOFTWARESER B:211 , GLY B:232 , ASN B:233 , HOH B:437binding site for residue EDO B 308
15AD6SOFTWAREASN B:65 , ARG B:98 , GLU B:104 , LYS B:112binding site for residue SO4 B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z0J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z0J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z0J)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z0J)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0j A   2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGAYTGEVSAEIAKDLNIEYVIIGHSERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       174       184       194       204       214       224       234       244    
                                                                                                                                                                                                  170|                                                                          
                                                                                                                                                                                                   174                                                                          


Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0j B   2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGAYTGEVSAEIAKDLNIEYVIIGHSERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 4Z0J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z0J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z0J)

(-) 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4z0j)
 

(-) 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
  4z0j
    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
  TPIS_PLAFA | Q07412
    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)
  5.3.1.1
    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
  TPIS_PLAFA | Q07412
    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
        TPIS_PLAFA | Q07412: 1lyx 1lzo 1m7o 1m7p 1o5x 1vga 1woa 1wob 1ydv 2fi6 2vfd 2vfe 2vff 2vfg 2vfh 2vfi 3psv 3psw 3pvf 3pwa 3py2 4ywi 4yxg 4z0s 4zz9 5bmw 5bmx 5bnk 5brb

(-) Related Entries Specified in the PDB File

2vfd 2vfe 2vff 2vfg 2vfh 4ywi 4yxg 4z0s