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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYO-EM STRUCTURE OF LACTATE DEHYDROGENASE (LDH) IN INHIBITOR-BOUND STATE
 
Authors :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, L. Earl, J. M S. Subramaniam
Date :  17 May 16  (Deposition) - 08 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lactate Dehydrogenase, Small Metabolic Complex, Small Molecule Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao, M. I. Davis R. Pragani, M. B. Boxer, L. A. Earl, J. L. Milne, S. Subramaniam
Breaking Cryo-Em Resolution Barriers To Facilitate Drug Discovery.
Cell V. 165 1698 2016
PubMed-ID: 27238019  |  Reference-DOI: 10.1016/J.CELL.2016.05.040

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE B CHAIN
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: BACTERIA
    Expression System Taxid: 2
    Gene: LDHB
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: LDH-B

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5K0Z)

(-) Sites  (0, 0)

(no "Site" information available for 5K0Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K0Z)

(-) 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 5K0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5K0Z)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee.......eeee....hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh...eeee...........eeee.....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0z A   1 ATLKEKLITPVTVPSNKITVVGVGQVGMACAISILGKGLCDELALVDVLEDKLKGEMMDLQHGSLFLQTHKIVADKDYAVTANSKIVVVTAGVLVQRNVNVFKFIIPQIVKYSPNCTILVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDTARFRYLMAERLGIHPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPAMGTDKDSENWKEVHKQVVESAYEVIRLKGYTNWAIGLSVAELCETMLKNLYRVHSVSTLVKGTYGIENDVFLSLPCVLSASGLTSVINQKLKDDEVAQLKKSADTLWSIQKDLKD 331
                                    10||      24        34        44        54        64        74        84        94  ||   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                     11|                                                                               97|                                                                                                                                                                                                                               
                                      16                                                                               108                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee.......eeee....hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh...eeee...........eeee.....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0z B   1 ATLKEKLITPVTVPSNKITVVGVGQVGMACAISILGKGLCDELALVDVLEDKLKGEMMDLQHGSLFLQTHKIVADKDYAVTANSKIVVVTAGVLVQRNVNVFKFIIPQIVKYSPNCTILVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDTARFRYLMAERLGIHPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPAMGTDKDSENWKEVHKQVVESAYEVIRLKGYTNWAIGLSVAELCETMLKNLYRVHSVSTLVKGTYGIENDVFLSLPCVLSASGLTSVINQKLKDDEVAQLKKSADTLWSIQKDLKD 331
                                    10||      24        34        44        54        64        74        84        94  ||   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                     11|                                                                               97|                                                                                                                                                                                                                               
                                      16                                                                               108                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee.......eeee....hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh...eeee...........eeee.....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0z C   1 ATLKEKLITPVTVPSNKITVVGVGQVGMACAISILGKGLCDELALVDVLEDKLKGEMMDLQHGSLFLQTHKIVADKDYAVTANSKIVVVTAGVLVQRNVNVFKFIIPQIVKYSPNCTILVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDTARFRYLMAERLGIHPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPAMGTDKDSENWKEVHKQVVESAYEVIRLKGYTNWAIGLSVAELCETMLKNLYRVHSVSTLVKGTYGIENDVFLSLPCVLSASGLTSVINQKLKDDEVAQLKKSADTLWSIQKDLKD 331
                                    10||      24        34        44        54        64        74        84        94  ||   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                     11|                                                                               97|                                                                                                                                                                                                                               
                                      16                                                                               108                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee.......eeee....hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh...eeee...........eeee.....hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhh.......eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0z D   1 ATLKEKLITPVTVPSNKITVVGVGQVGMACAISILGKGLCDELALVDVLEDKLKGEMMDLQHGSLFLQTHKIVADKDYAVTANSKIVVVTAGVLVQRNVNVFKFIIPQIVKYSPNCTILVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDTARFRYLMAERLGIHPTSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPAMGTDKDSENWKEVHKQVVESAYEVIRLKGYTNWAIGLSVAELCETMLKNLYRVHSVSTLVKGTYGIENDVFLSLPCVLSASGLTSVINQKLKDDEVAQLKKSADTLWSIQKDLKD 331
                                    10||      24        34        44        54        64        74        84        94  ||   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                     11|                                                                               97|                                                                                                                                                                                                                               
                                      16                                                                               108
   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 5K0Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K0Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K0Z)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Sites
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  Cis Peptide Bonds
    Asn A:137 - Pro A:138   [ RasMol ]  
    Asn B:137 - Pro B:138   [ RasMol ]  
    Asn C:137 - Pro C:138   [ RasMol ]  
    Asn D:137 - Pro D:138   [ RasMol ]  
 

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  5k0z
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  LDHB_CHICK | P00337
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

5k10 5k11 5k12