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 ANCESTRAL APICOMPLEXAN MALATE DEHYDROGENASE WITH LACTATE.
 
Authors :  J. I. Boucher, J. R. Jacobowitz, B. C. Beckett, S. Classen, D. L. Theobal
Date :  19 May 14  (Deposition) - 02 Jul 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ancestral Sequence Reconstruction, Dehydrogenase, Apicomplexa, Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Boucher, J. R. Jacobowitz, B. C. Beckett, S. Classen, D. L. Theobald
An Atomic-Resolution View Of Neofunctionalization In The Evolution Of Apicomplexan Lactate Dehydrogenases.
Elife V. 3 02304 2014
PubMed-ID: 24966208  |  Reference-DOI: 10.7554/ELIFE.02304

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3 (PLYSS)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: APICOMPLEXA
    Organism Taxid: 5794

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
12OP4Ligand/Ion(2S)-2-HYDROXYPROPANOIC ACID
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ASN A:14 , ILE A:15 , PHE A:34 , ASP A:35 , ILE A:36 , VAL A:37 , MET A:40 , TYR A:67 , THR A:79 , ALA A:80 , GLY A:81 , ILE A:105 , VAL A:125 , THR A:126 , ASN A:127 , MET A:150 , LEU A:154 , HIS A:182 , 2OP A:402 , HOH A:509 , HOH A:510 , HOH A:553 , HOH A:587binding site for residue NAI A 401
2AC2SOFTWAREASN A:127 , ARG A:158 , HIS A:182 , GLY A:225 , NAI A:401 , HOH A:588binding site for residue 2OP A 402
3AC3SOFTWAREGLY B:13 , ASN B:14 , ILE B:15 , PHE B:34 , ASP B:35 , ILE B:36 , VAL B:37 , MET B:40 , TYR B:67 , THR B:79 , ALA B:80 , GLY B:81 , ILE B:82 , PRO B:83 , LEU B:98 , ASN B:102 , ILE B:105 , VAL B:125 , ASN B:127 , MET B:150 , LEU B:154 , HIS B:182 , ALA B:237 , PRO B:241 , 2OP B:402 , HOH B:509 , HOH B:512 , HOH B:513 , HOH B:520 , HOH B:534 , HOH B:543 , HOH B:586 , HOH B:597binding site for residue NAI B 401
4AC4SOFTWARETRP B:93 , ARG B:95 , ASN B:127 , ARG B:158 , HIS B:182 , GLY B:225 , NAI B:401 , HOH B:525binding site for residue 2OP B 402
5AC5SOFTWAREGLY C:13 , ASN C:14 , ILE C:15 , ASP C:35 , ILE C:36 , VAL C:37 , MET C:40 , THR C:79 , ALA C:80 , GLY C:81 , ILE C:82 , PRO C:83 , LEU C:98 , ILE C:105 , VAL C:125 , THR C:126 , ASN C:127 , MET C:150 , LEU C:154 , HIS C:182 , ALA C:237 , PRO C:241 , 2OP C:402 , HOH C:507 , HOH C:525 , HOH C:531 , HOH C:538 , HOH C:554 , HOH C:579 , HOH C:589 , HOH C:590 , HOH C:596binding site for residue NAI C 401
6AC6SOFTWARETRP C:93 , ARG C:95 , ASN C:127 , ARG C:158 , HIS C:182 , GLY C:225 , ALA C:237 , NAI C:401 , HOH C:608binding site for residue 2OP C 402
7AC7SOFTWAREGLY D:13 , ASN D:14 , ILE D:15 , PHE D:34 , ASP D:35 , ILE D:36 , VAL D:37 , MET D:40 , TYR D:67 , THR D:79 , ALA D:80 , GLY D:81 , ILE D:105 , VAL D:125 , ASN D:127 , MET D:150 , LEU D:154 , HIS D:182 , ALA D:237 , PRO D:241 , 2OP D:402 , HOH D:516 , HOH D:517 , HOH D:551 , HOH D:591binding site for residue NAI D 401
8AC8SOFTWAREASN D:127 , ARG D:158 , HIS D:182 , NAI D:401 , HOH D:589 , HOH D:592binding site for residue 2OP D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:127 -Pro A:128
2Asn B:127 -Pro B:128
3Asn C:127 -Pro C:128
4Asn D:127 -Pro D:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLV)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plv A   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKL 321
                                    12        22        32        42        52        62        72        82|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316     
                                                                                                          82|                                                                                                                                                                                                                                
                                                                                                           97                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plv B   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plv C   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        


Chain D from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plv D   2 TQRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKL 321
                                    11        21        31        41        51        61        71        81||     104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       
                                                                                                           82|                                                                                                                                                                                                                                 
                                                                                                            96
   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 4PLV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PLV)

 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
    2OP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAI  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:127 - Pro A:128   [ RasMol ]  
    Asn B:127 - Pro B:128   [ RasMol ]  
    Asn C:127 - Pro C:128   [ RasMol ]  
    Asn D:127 - Pro D:128   [ 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
  4plv
    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
  A0A075B5H0_9 | A0A075B5H0
    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)
  (no 'Enzyme Classificator' available)
    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
  A0A075B5H0_9 | A0A075B5H0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A075B5H0_9 | A0A075B5H0: 4plt 4ply

(-) Related Entries Specified in the PDB File

4plc 4plf 4plg 4plh 4plt 4plw 4ply 4plz