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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LACTATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM
 
Authors :  D. Chattopadhyay, W. J. Cook
Date :  25 Oct 13  (Deposition) - 17 Dec 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Apoenzyme Structure, 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, C, D
    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
    Gene: CGD7_480, LDH1
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 353152
    Strain: IOWA II

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4ND5)

(-) Sites  (0, 0)

(no "Site" information available for 4ND5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ND5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141
3Asn C:140 -Pro C:141
4Asn D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ND5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ND5)

(-) Exons   (0, 0)

(no "Exon" information available for 4ND5)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee...hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eeeeeeeeee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nd5 A   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITALLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLD  330
                               ||   27        37        48        58        68    ||  77   ||   88        98|      121       131||     140       150       160       170       180       190       200      209B|||   218B       228       238     ||246       256       266       276      |287       297 ||    308       318       328  
                              20|                      46|                      73A|      81|             98|                132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                             
                               22                       48                       73B       83             112                 132B                                                                          209B|||   218B                       244B|                                     285            301                             
                                                                                                                                                                                                             210A||                               244C                                                                                    
                                                                                                                                                                                                              210B|                                                                                                                       
                                                                                                                                                                                                                212                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh........eeee.hhhhhh...eeee...hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nd5 B   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITALLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVL  329
                               ||   27        37        48        58        68    ||  77   ||   88        98|      121       131||     140       150       160       170       180       190       200      209B|||   218B       228       238     ||246       256       266       276      |287       297 ||    308       318       328 
                              20|                      46|                      73A|      81|             98|                132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                            
                               22                       48                       73B       83             112                 132B                                                                          209B|||   218B                       244B|                                     285            301                            
                                                                                                                                                                                                             210A||                               244C                                                                                   
                                                                                                                                                                                                              210B|                                                                                                                      
                                                                                                                                                                                                                212                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee...hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4nd5 C   18 IERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITALLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVL  329
                              ||    28        38       |49        59        69   ||   78  ||    89       112       122      132A|      141       151       161       171       181       191       201      210A||     219       229       239    |||247       257       267       277     ||288       298||     309       319       329
                             20|                      46|                      73A|      81|             98|                132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                            
                              22                       48                       73B       83             112                 132B                                                                          209B|||   218B                       244B|                                     285            301                            
                                                                                                                                                                                                            210A||                               244C                                                                                   
                                                                                                                                                                                                             210B|                                                                                                                      
                                                                                                                                                                                                               212                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee...hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhhhee...hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nd5 D   18 IERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITALLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISK  327
                              ||    28        38       |49        59        69   ||   78  ||    89       112       122      132A|      141       151       161       171       181       191       201      210A||     219       229       239    |||247       257       267       277     ||288       298||     309       319        
                             20|                      46|                      73A|      81|             98|                132A|                                                                         209A||||  218A|                      244A||                                    283|           299|                          
                              22                       48                       73B       83             112                 132B                                                                          209B|||   218B                       244B|                                     285            301                          
                                                                                                                                                                                                            210A||                               244C                                                                                 
                                                                                                                                                                                                             210B|                                                                                                                    
                                                                                                                                                                                                               212
   Legend:   → Mismatch (orange background)
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    → 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 ; only for superseded entry 2FRM: 2,8)

(no "SCOP Domain" information available for 4ND5, only for superseded entry 2FRM replaced by 4ND5)

(-) CATH Domains  (0, 0 ; only for superseded entry 2FRM: 2,8)

(no "CATH Domain" information available for 4ND5, only for superseded entry 2FRM replaced by 4ND5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ND5)

(-) Gene Ontology  (7, 7)

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        Q5CYZ2_CRYPI | Q5CYZ2: 2fn7 4nd1 4nd2 4nd3 4nd4

(-) Related Entries Specified in the PDB File

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