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(-) Description

Title :  L-LACTATE DEHYDROGENASE FROM RABBIT MUSCLE WITH THE INHIBITOR 6DHNAD
 
Authors :  K. M. Meneely, G. R. Moran, A. L. Lamb
Date :  21 Jun 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lactate Dehydrogenase, Inhibitor, 6Dhnad, Beta- 6-Dihydronicotimide Adenine Dinucleotide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Beaupre, J. V. Roman, M. R. Hoag, K. M. Meneely, N. R. Silvaggi, A. L. Lamb, G. R. Moran
Ligand Binding Phenomena That Pertain To The Metabolic Function Of Renalase.
Arch. Biochem. Biophys. V. 612 46 2016
PubMed-ID: 27769837  |  Reference-DOI: 10.1016/J.ABB.2016.10.011

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: LDH-A,LDH MUSCLE SUBUNIT,LDH-M

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
16V04Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(5-AMINOCARBONYL-2~{H}-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYLHYDROGEN PHOSPHATE
2SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:28 , ALA A:29 , VAL A:30 , ASP A:51 , VAL A:52 , MET A:53 , THR A:94 , ALA A:95 , GLY A:96 , ALA A:97 , ARG A:98 , GLN A:99 , ILE A:115 , ILE A:119 , VAL A:135 , SER A:136 , ASN A:137 , THR A:247 , ILE A:251 , HOH A:506 , HOH A:516 , HOH A:522 , HOH A:524 , HOH A:525 , HOH A:556 , HOH A:569 , HOH A:577binding site for residue 6V0 A 401
2AC2SOFTWAREGLU A:284 , ASP A:320 , HOH B:511binding site for residue SO4 A 402
3AC3SOFTWAREARG A:170 , HIS A:185 , HOH A:505 , HOH A:547 , HOH A:578 , HIS D:185binding site for residue SO4 A 403
4AC4SOFTWAREGLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , MET B:53 , THR B:94 , ALA B:95 , GLY B:96 , ARG B:98 , VAL B:135 , SER B:136 , ASN B:137 , SER B:160 , HIS B:192 , THR B:247 , ILE B:251 , HOH B:510 , HOH B:532 , HOH B:535 , HOH B:541 , HOH B:569binding site for residue 6V0 B 401
5AC5SOFTWAREARG B:170 , HIS B:185 , HOH B:501 , HOH B:508 , HOH B:509 , HOH B:585 , HIS C:185binding site for residue SO4 B 402
6AC6SOFTWAREGLY C:28 , ALA C:29 , VAL C:30 , ASP C:51 , VAL C:52 , MET C:53 , LYS C:56 , THR C:94 , ALA C:95 , GLY C:96 , ALA C:97 , ARG C:98 , ILE C:115 , ILE C:119 , VAL C:135 , ASN C:137 , SER C:160 , LEU C:164 , HIS C:192 , THR C:247 , ILE C:251 , HOH C:516 , HOH C:518 , HOH C:521 , HOH C:522 , HOH C:523 , HOH C:543 , HOH C:569binding site for residue 6V0 C 401
7AC7SOFTWAREHIS B:185 , ARG C:170 , HIS C:185 , HOH C:509 , HOH C:524 , HOH C:527binding site for residue SO4 C 402
8AC8SOFTWAREGLY D:26 , VAL D:27 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , THR D:94 , ALA D:95 , GLY D:96 , ALA D:97 , ARG D:98 , LEU D:108 , ILE D:115 , ILE D:119 , VAL D:135 , ASN D:137 , SER D:160 , LEU D:164 , HIS D:192 , THR D:247 , ILE D:251 , HOH D:505 , HOH D:523 , HOH D:528 , HOH D:537 , HOH D:547 , HOH D:548binding site for residue 6V0 D 401
9AC9SOFTWAREHIS A:185 , ARG D:170 , HIS D:185 , HOH D:510 , HOH D:524 , HOH D:530 , HOH D:583binding site for residue SO4 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KKC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:137 -Pro A:138
2Asn B:137 -Pro B:138
3Asn C:137 -Pro C:138
4Asn D:137 -Pro D:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KKC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KKC)

(-) Exons   (0, 0)

(no "Exon" information available for 5KKC)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee.......eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkc A   1 AALKDQLIHNLLKVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVAGVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCVLGQNGISDVVKVTLTSEEEAHLKKSADTLWGIQKELQF 331
                                    10  ||    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
                                       13|                                                                                                                                                                                                                                                                                                                          
                                        17                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee......hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkc B   2 ALKDQLIHNLLKEEHVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVAGVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCVLGQNGISDVVKVTLTSEEEAHLKKSADTLWGIQKELQF 331
                                    11        21        31        41        51        61        71        81        91      |111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
                                                                                                                           98|                                                                                                                                                                                                                              
                                                                                                                           109                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheee........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.eeeeee.......eeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkc C   2 ALKDQLIHNLLKHVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVAGVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCVLGQNGISDVVKVTLTSEEEAHLKKSADTLWGIQKEL 329
                                    11 ||     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      
                                      13|                                                                                                                                                                                                                                                                                                                         
                                       16                                                                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkc D   1 AALKDQLIHNLLKEEHVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVAGVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCVLGQNGISDVVKVTLTSEEEAHLKKSADTLWGIQKEL 329
                                    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
   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 5KKC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KKC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KKC)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kkc
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        LDHA_RABIT | P13491: 3h3f 4i8x 4i9h 4i9n 4i9u 5nqb 5nqq

(-) Related Entries Specified in the PDB File

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