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(-) Description

Title :  CRYSTAL STRUCTURE OF COFACTOR(NAD+) BOUND 3-PHOSPHOGLYCERATE DEHYDROGENASE IN ENTAMOEBA HISTOLYTICA
 
Authors :  R. K. Singh, S. Gourinath
Date :  11 Nov 13  (Deposition) - 08 Oct 14  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Singh, I. Raj, R. Pujari, S. Gourinath
Crystal Structures And Kinetics Of Type Iii 3-Phosphoglycerate Dehydrogenase Reveal Catalysis By Lysine
Febs J. V. 281 5498 2014
PubMed-ID: 25294608  |  Reference-DOI: 10.1111/FEBS.13091

(-) Compounds

Molecule 1 - D-3-PHOSPHOGLYCERATE DEHYDROGENASE, PUTATIVE
    Chains: A, B
    EC Number: 1.1.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EHPGDH, EHI_060860
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759
    Synonym: D-PHOSPHOGLYCERATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:78 , ASN A:102 , VAL A:106 , GLY A:139 , GLY A:141 , TYR A:142 , VAL A:143 , ASP A:162 , PRO A:163 , PHE A:164 , HIS A:187 , LEU A:188 , PRO A:189 , GLU A:193 , THR A:194 , THR A:215 , ALA A:216 , ARG A:217 , ASP A:241 , LYS A:263 , GLY A:265 , ALA A:266 , FMT A:402 , HOH A:507 , HOH A:519BINDING SITE FOR RESIDUE NAD A 401
2AC2SOFTWAREARG A:75 , ALA A:78 , GLY A:79 , ARG A:217 , LYS A:263 , NAD A:401BINDING SITE FOR RESIDUE FMT A 402
3AC3SOFTWAREARG B:75 , GLY B:77 , ALA B:78 , GLY B:79 , ASN B:102 , ARG B:217 , GOL B:403BINDING SITE FOR RESIDUE FMT B 401
4AC4SOFTWAREGLY B:141 , TYR B:142 , VAL B:143 , GLY B:144 , HIS B:187BINDING SITE FOR RESIDUE TRS B 402
5AC5SOFTWARELYS B:9 , ARG B:55 , SER B:56 , ARG B:75 , ALA B:266 , FMT B:401BINDING SITE FOR RESIDUE GOL B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NJO)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh..eeeeee.....hhhhhhh....eeee.....hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhh.eeeee...........hhhhhhhhh.eeee............hhhhhh......eeee..hhhhhhhhhhhhhhhhh...eeee......hhhhhhh...eee........hhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njo A  -1 ASMKIVVITEKPFAENAVKGIREILEKAGHEVVMIEKYKKKEDVIERIKDADGVIVRSDKIDEEIIKAGEKVKIIVRAGAGYDNIDIEACNQGKIVVMNTPGQNRNGVAELCIGMMIFGFRKGFKEGKGRELKDKTLGICGCGYVGKRVKEIAEGIGMKIKVYDPFITTENQVKKIEELFEECQVISLHLPLTKETKGKIGYELIKKLPYGGMICNTARKEIIDEEGLIRIMREREDLIYITDVAPTSKVFNNEFKGRFFATPIKIGAETEESNINAGMAAASQICDFFTNGTVKFQVNKFL 300
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  


Chain B from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeee.....hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhhh.eeeee...........hhhhhhhhh.eeee............hhhhhh......eeee..hhhhhhhhhhhhhhhhh...eeee......hhhhhhh...eee........hhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4njo B  -1 ASMKIVVITEKPFAENAVKGIREILEKAGHEVVMIEKYKKKEDVIERIKDADGVIVRSDKIDEEIIKAGEKVKIIVRAGAGYDNIDIEACNQGKIVVMNTPGQNRNGVAELCIGMMIFGFRKGFKEGKGRELKDKTLGICGCGYVGKRVKEIAEGIGMKIKVYDPFITTENQVKKIEELFEECQVISLHLPLTKETKGKIGYELIKKLPYGGMICNTARKEIIDEEGLIRIMREREDLIYITDVAPTSKVFNNEFKGRFFATPIKIGAETEESNINAGMAAASQICDFFTNGTVKFQVNKFL 300
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
   Legend:   → Mismatch (orange background)
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  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 4NJO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q76KF5_ENTHI | Q76KF5: 4nfy 4njm

(-) Related Entries Specified in the PDB File

4njm