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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LACTATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM COMPLEXED WITH SUBSTRATE (PYRUVIC ACID) AND COFACTOR ANALOG (3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE)
 
Authors :  D. Chattopadhyay, W. J. Cook
Date :  25 Oct 13  (Deposition) - 17 Dec 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Dehydrogenase, Nad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Cook, O. Senkovich, A. Hernandez, H. Speed, D. Chattopadhyay
Biochemical And Structural Characterization Of Cryptosporidium Parvum Lactate Dehydrogenase.
Int. J. Biol. Macromol. V. 74C 608 2014
PubMed-ID: 25542170  |  Reference-DOI: 10.1016/J.IJBIOMAC.2014.12.019

(-) Compounds

Molecule 1 - LACTATE DEHYDROGENASE, ADJACENT GENE ENCODES PREDICTED MALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 17-337
    Gene: CGD7_480, LDH1
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 353152
    Strain: IOWA II

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1A3D2Ligand/Ion3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1A3D4Ligand/Ion3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
2GOL6Ligand/IonGLYCEROL
3PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , GLN A:31 , ILE A:32 , ASP A:53 , ILE A:54 , THR A:97 , ALA A:98 , SER A:99 , ILE A:119 , ILE A:138 , ASN A:140 , MET A:163 , LEU A:167 , HIS A:195 , GLU A:223 , ALA A:246 , PRO A:250 , PYR A:402 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:522 , HOH A:523 , HOH A:526 , HOH A:549 , HOH A:566 , HOH A:568 , HOH A:573 , HOH A:583 , HOH A:591 , HOH A:609BINDING SITE FOR RESIDUE A3D A 401
2AC2SOFTWAREARG A:109 , ASN A:140 , LEU A:167 , ARG A:171 , HIS A:195 , TRP A:236 , THR A:245 , A3D A:401 , HOH A:501BINDING SITE FOR RESIDUE PYR A 402
3AC3SOFTWAREPRO A:201 , THR A:203 , GLU A:311 , LEU A:314 , HOH A:603 , HOH A:638BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREPRO A:141 , ASP A:143 , VAL A:144 , GLY A:194 , HIS A:195 , GLU A:321 , VAL A:322 , ILE A:325 , HOH A:555 , HOH A:560BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREGLY B:30 , GLN B:31 , ILE B:32 , ASP B:53 , ILE B:54 , THR B:97 , ALA B:98 , SER B:99 , ILE B:119 , SER B:122 , ILE B:138 , ASN B:140 , MET B:163 , LEU B:167 , HIS B:195 , ALA B:246 , PRO B:250 , PYR B:402 , HOH B:507 , HOH B:508 , HOH B:526 , HOH B:537 , HOH B:538 , HOH B:587 , HOH B:632 , HOH B:646 , HOH B:668BINDING SITE FOR RESIDUE A3D B 401
6AC6SOFTWAREARG B:109 , ASN B:140 , LEU B:167 , ARG B:171 , HIS B:195 , TRP B:236 , THR B:245 , A3D B:401 , HOH B:509BINDING SITE FOR RESIDUE PYR B 402
7AC7SOFTWAREVAL B:200 , PRO B:201 , THR B:203 , GLU B:311 , HOH B:523 , HOH B:582BINDING SITE FOR RESIDUE GOL B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ND2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ND2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ND2)

(-) Exons   (0, 0)

(no "Exon" information available for 4ND2)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nd2 A   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
                               ||   27        37        48        58        68    ||  77   ||   88        98    || 109       119       129  ||   138       148       158       168       178       188       198       208|||||  217||     226       236      244C       254       264       274       285       295   ||  306       316       326       
                              20|                      46|                      73A|      81|                 103|                       132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                                
                               22                       48                       73B       83                  105                        132B                                                                          209B|||   218B                       244B|                                     285            301                                
                                                                                                                                                                                                                         210A||                               244C                                                                                       
                                                                                                                                                                                                                          210B|                                                                                                                          
                                                                                                                                                                                                                            212                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nd2 B   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
                               ||   27        37        48        58        68    ||  77   ||   88        98    || 109       119       129  ||   138       148       158       168       178       188       198       208|||||  217||     226       236      244C       254       264       274       285       295   ||  306       316       326       
                              20|                      46|                      73A|      81|                 103|                       132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                                
                               22                       48                       73B       83                  105                        132B                                                                          209B|||   218B                       244B|                                     285            301                                
                                                                                                                                                                                                                         210A||                               244C                                                                                       
                                                                                                                                                                                                                          210B|                                                                                                                          
                                                                                                                                                                                                                            212
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0 ; only for superseded entry 2EWD: 2,4)

(no "SCOP Domain" information available for 4ND2, only for superseded entry 2EWD replaced by 4ND2)

(-) CATH Domains  (0, 0 ; only for superseded entry 2EWD: 2,4)

(no "CATH Domain" information available for 4ND2, only for superseded entry 2EWD replaced by 4ND2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ND2)

(-) Gene Ontology  (7, 7)

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