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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  KNOWLEDGE-BASED MODELING OF THE D-LACTATE DEHYDROGENASE THREE-DIMENSIONAL STRUCTURE
 
Authors :  C. Vinals
Date :  25 Jan 95  (Deposition) - 31 Mar 95  (Release) - 31 Mar 95  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Oxidoreductase (Choh(D)-Nad+(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Vinals, X. De Bolle, E. Depiereux, E. Feytmans
Knowledge-Based Modeling Of The D-Lactate Dehydrogenase Three-Dimensional Structure.
Proteins V. 21 307 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-LACTATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.28
    Engineered: YES
    Organism Scientific: BACILLUS DELBRUECKII SSP. BULGARICUS

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PYR1Ligand/IonPYRUVIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1DLD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DLD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DLD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DLD)

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.LDHD_LACDA149-176  1A:149-176
2D_2_HYDROXYACID_DH_2PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2.LDHD_LACDA196-218  1A:196-218
3D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.LDHD_LACDA225-241  1A:225-241

(-) Exons   (0, 0)

(no "Exon" information available for 1DLD)

(-) Sequences/Alignments

Theoretical Model
   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:333
 aligned with LDHD_LACDA | P26297 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
           LDHD_LACDA     1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYTAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVIGTGHIGQVFMQIMEGFGAKVIAYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKVG 333
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhh...............hhhhhhhh..eeee...........hhhhh........eeee....hhh..hhhhhhh..eee......hhhhhhhhhhhhhhh............................eeeeee.....hhhhhhhhhhh.eeeeee.................hhhhhhh..eeee.............hhhhhh......eee........hhhhhhhhhh.....eee................................eee........hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        -------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dld A   1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYTAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAAAILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVIGTGHIGQVFMQIMEGFGAKVITYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKVG 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   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 1DLD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1DLD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DLD)

(-) Gene Ontology  (6, 6)

Theoretical Model(hide GO term definitions)
Chain A   (LDHD_LACDA | P26297)
molecular function
    GO:0008720    D-lactate dehydrogenase activity    Catalysis of the reaction: (R)-lactate + NAD(+) = H(+) + NADH + pyruvate.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LDHD_LACDA | P26297: 1j49 1j4a

(-) Related Entries Specified in the PDB File

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