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(-) Description

Title :  LACTATE DEHYDROGENASE A IN COMPLEX WITH A TRISUBSTITUTED PIPERIDINE-2, 4-DIONE INHIBITOR GNE-140
 
Authors :  Y. Li, Z. Chen, C. Eigenbrot
Date :  18 May 15  (Deposition) - 18 May 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase Inhibitor Complex, Ldha-G02792140, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Boudreau, H. E. Purkey, A. Hitz, K. Robarge, D. Peterson, S. Labadie M. Kwong, R. Hong, M. Gao, C. Del Nagro, R. Pusapati, S. Ma, L. Salphati J. Pang, A. Zhou, T. Lai, Y. Li, Z. Chen, B. Wei, I. Yen, S. Sideris, M. Mccleland, R. Firestein, L. Corson, A. Vanderbilt, S. Williams, A. Daemen, M. Belvin, C. Eigenbrot, P. K. Jackson, S. Malek, G. Hatzivassiliou, D. Sampath, M. Evangelista, T. O'Brien
Metabolic Plasticity Underpins Innate And Acquired Resistance To Ldha Inhibition.
Nat. Chem. Biol. V. 12 779 2016
PubMed-ID: 27479743  |  Reference-DOI: 10.1038/NCHEMBIO.2143

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LDHA, PIG19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LDH-A,CELL PROLIFERATION-INDUCING GENE 19 PROTEIN,LDH MUSCLE SUBUNIT,LDH-M,RENAL CARCINOMA ANTIGEN NY-REN-59

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1GN04Ligand/Ion(2~{R})-5-(2-CHLOROPHENYL)SULFANYL-2-(4-MORPHOLIN-4-YLPHENYL)-4-OXIDANYL-2-THIOPHEN-3-YL-1,3-DIHYDROPYRIDIN-6-ONE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO47Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:28 , ALA A:29 , VAL A:30 , ASP A:51 , VAL A:52 , ILE A:53 , THR A:94 , ALA A:95 , GLY A:96 , ARG A:98 , ILE A:115 , VAL A:135 , ASN A:137 , LEU A:164 , HIS A:192 , ILE A:251 , GN0 A:405 , HOH A:506 , HOH A:511 , HOH A:515 , HOH A:524 , HOH A:528binding site for residue NAD A 401
02AC2SOFTWAREHIS A:185 , ARG C:170 , HIS C:185 , HOH C:561binding site for residue SO4 A 402
03AC3SOFTWAREARG A:170 , HIS A:185 , HOH A:508 , HOH A:529 , HOH A:549 , LEU C:182 , HIS C:185binding site for residue SO4 A 403
04AC4SOFTWARETRP A:147 , PRO A:153 , LYS A:154binding site for residue SO4 A 404
05AC5SOFTWAREASN A:137 , ASP A:165 , ARG A:168 , HIS A:192 , GLY A:193 , ASP A:194 , ALA A:237 , TYR A:238 , ILE A:241 , GLY A:245 , THR A:247 , NAD A:401binding site for residue GN0 A 405
06AC6SOFTWAREGLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , ILE B:53 , THR B:94 , ALA B:95 , GLY B:96 , ARG B:98 , ILE B:115 , ILE B:119 , VAL B:135 , ASN B:137 , LEU B:164 , HIS B:192 , ILE B:251 , GN0 B:404 , HOH B:502 , HOH B:504 , HOH B:518 , HOH B:538 , HOH B:539binding site for residue NAD B 401
07AC7SOFTWAREARG B:170 , HIS B:185 , HOH B:536 , HOH B:546 , HOH B:562 , LEU D:182 , HIS D:185binding site for residue SO4 B 402
08AC8SOFTWARETRP B:147 , PRO B:153 , LYS B:154binding site for residue SO4 B 403
09AC9SOFTWAREARG B:98 , ASN B:137 , LEU B:164 , ASP B:165 , ARG B:168 , HIS B:192 , GLY B:193 , ALA B:237 , TYR B:238 , ILE B:241 , GLY B:245 , THR B:247 , NAD B:401binding site for residue GN0 B 404
10AD1SOFTWAREGLY C:28 , ALA C:29 , VAL C:30 , ASP C:51 , VAL C:52 , ILE C:53 , THR C:94 , ALA C:95 , GLY C:96 , ARG C:98 , ILE C:119 , VAL C:135 , ASN C:137 , HIS C:192 , THR C:247 , GN0 C:403 , HOH C:507 , HOH C:511 , HOH C:520 , HOH C:526 , HOH C:557binding site for residue NAD C 401
11AD2SOFTWARETRP C:147 , PRO C:153 , LYS C:154 , HOH C:543binding site for residue SO4 C 402
12AD3SOFTWAREARG C:98 , ASN C:137 , LEU C:164 , ASP C:165 , ARG C:168 , HIS C:192 , GLY C:193 , ALA C:237 , TYR C:238 , ILE C:241 , THR C:247 , NAD C:401 , HOH C:573binding site for residue GN0 C 403
13AD4SOFTWAREGLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , ILE D:53 , THR D:94 , ALA D:95 , GLY D:96 , ILE D:115 , PHE D:118 , ILE D:119 , VAL D:135 , ASN D:137 , SER D:160 , HIS D:192 , THR D:247 , GN0 D:403 , HOH D:510 , HOH D:522 , HOH D:529 , HOH D:534 , HOH D:538binding site for residue NAD D 401
14AD5SOFTWARELEU B:182 , HIS B:185 , ARG D:170 , HIS D:185 , HOH D:543 , HOH D:564binding site for residue SO4 D 402
15AD6SOFTWAREGLN D:99 , ASN D:137 , ASP D:165 , ARG D:168 , HIS D:192 , GLY D:193 , ASP D:194 , ALA D:237 , TYR D:238 , ILE D:241 , GLY D:245 , THR D:247 , NAD D:401 , HOH D:541binding site for residue GN0 D 403

(-) SS Bonds  (0, 0)

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

(-) 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 4ZVV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZVV)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.hhh.ee..eehhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zvv A   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    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 


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eee..hhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zvv B   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    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 


Chain C from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eee..hhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.....ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zvv C   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    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 


Chain D from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh..............hhhh.ee..eehhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zvv D   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    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 4ZVV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  4zvv
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  LDHA_HUMAN | P00338
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDHA_HUMAN | P00338: 1i10 4ajp 4jnk 4l4r 4l4s 4m49 4ojn 4okn 4qo7 4qo8 4qsm 4qt0 4r68 4r69 4rls 5ixs 5ixy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZVV)