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(-) Description

Title :  PKM2 IN COMPLEX WITH COMPOUND 2
 
Authors :  Y. Matsui, H. Hanzawa
Date :  27 Jan 17  (Deposition) - 31 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Activator, Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matsui, I. Yasumatsu, T. Asahi, T. Kitamura, K. Kanai, O. Ubukata, H. Hayasaka, S. Takaishi, H. Hanzawa, S. Katakura
Discovery And Structure-Guided Fragment-Linking Of 4-(2, 3-Dichlorobenzoyl)-1-Methyl-Pyrrole-2-Carboxamide As A Pyruvate Kinase M2 Activator
Bioorg. Med. Chem. V. 25 3540 2017
PubMed-ID: 28511909  |  Reference-DOI: 10.1016/J.BMC.2017.05.004

(-) Compounds

Molecule 1 - PYRUVATE KINASE PKM
    Chains: A, B, C, D
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PKM, OIP3, PK2, PK3, PKM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC THYROID HORMONE-BINDING PROTEIN,CTHBP,OPA- INTERACTING PROTEIN 3,OIP-3,PYRUVATE KINASE 2/3,PYRUVATE KINASE MUSCLE ISOZYME,THYROID HORMONE-BINDING PROTEIN 1,THBP1,TUMOR M2-PK, P58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
17XX4Ligand/Ion4-[2,3-BIS(CHLORANYL)PHENYL]CARBONYL-1-METHYL-PYRROLE-2-CARBOXAMIDE
2FBP4Ligand/IonBETA-FRUCTOSE-1,6-DIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:431 , THR A:432 , LYS A:433 , SER A:434 , ARG A:436 , SER A:437 , TRP A:482 , ARG A:489 , GLY A:514 , ARG A:516 , PRO A:517 , GLY A:518 , SER A:519 , GLY A:520 , PHE A:521 , THR A:522 , HOH A:702 , HOH A:758 , HOH A:773binding site for residue FBP A 601
2AC2SOFTWAREPHE A:26 , LEU A:353 , ALA A:388 , ILE A:389 , TYR A:390 , GLN A:393 , LEU A:394 , GLU A:397 , HOH A:713 , HOH A:728 , PHE B:26 , LYS B:311 , 7XX B:602binding site for residue 7XX A 602
3AC3SOFTWAREGLU A:223 , LEU B:431 , THR B:432 , LYS B:433 , SER B:434 , SER B:437 , TRP B:482 , ARG B:489 , GLY B:514 , ARG B:516 , PRO B:517 , GLY B:518 , SER B:519 , GLY B:520 , PHE B:521 , THR B:522 , HOH B:771 , HOH B:775 , HOH B:783binding site for residue FBP B 601
4AC4SOFTWAREPHE A:26 , LYS A:311 , 7XX A:602 , PHE B:26 , LEU B:353 , ASP B:354 , ALA B:388 , ILE B:389 , TYR B:390 , GLN B:393 , LEU B:394 , GLU B:397 , HOH B:745 , HOH B:802binding site for residue 7XX B 602
5AC5SOFTWARELEU C:431 , THR C:432 , LYS C:433 , SER C:434 , SER C:437 , TRP C:482 , ARG C:489 , GLY C:514 , ARG C:516 , PRO C:517 , GLY C:518 , SER C:519 , GLY C:520 , PHE C:521 , THR C:522 , HOH C:705 , HOH C:773 , HOH C:790 , HOH C:800binding site for residue FBP C 601
6AC6SOFTWAREPHE C:26 , LEU C:353 , ASP C:354 , ALA C:388 , ILE C:389 , TYR C:390 , GLN C:393 , LEU C:394 , GLU C:397 , HOH C:725 , PHE D:26 , LYS D:311 , 7XX D:602binding site for residue 7XX C 602
7AC7SOFTWARELEU D:431 , THR D:432 , LYS D:433 , SER D:434 , SER D:437 , TRP D:482 , ARG D:489 , GLY D:514 , ARG D:516 , PRO D:517 , GLY D:518 , SER D:519 , GLY D:520 , PHE D:521 , THR D:522 , HOH D:704 , HOH D:707 , HOH D:744 , HOH D:755binding site for residue FBP D 601
8AC8SOFTWAREPHE C:26 , LYS C:311 , 7XX C:602 , PHE D:26 , LEU D:353 , ASP D:354 , ALA D:388 , ILE D:389 , TYR D:390 , LEU D:394 , GLU D:397 , HOH D:800 , HOH D:805binding site for residue 7XX D 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X1V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X1V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X1V)

(-) Exons   (0, 0)

(no "Exon" information available for 5X1V)

(-) 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:512
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee.....ee...........eee....eeeee.hhhhhh.....eee..............eeee....eeeee..eeeeee.eee....eee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1v A  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  ||   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529  
                                                                                                                                                                                                      186|                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                       193                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee.....ee......eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeeeee.eee....eee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1v B  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       123||     138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528   
                                                                                                                                        124|                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                         130                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee..................eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1v C  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    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       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523        


Chain D from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhh.............eeeee......hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh...........eeeee...........eee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee...eeeeeeee.eee.....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x1v D  14 QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP 531
                                    23        33        43        53        63        73        83        93       103       113       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530 
                                                                                                                                      122|                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                       130
   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 5X1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X1V)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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  5x1v
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  KPYM_HUMAN | P14618
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 Related Entries

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

UniProtKB/Swiss-Prot
        KPYM_HUMAN | P14618: 1t5a 1zjh 3bjf 3bjt 3g2g 3gqy 3gr4 3h6o 3me3 3srd 3srf 3srh 3u2z 4b2d 4fxf 4fxj 4g1n 4jpg 4qg6 4qg8 4qg9 4qgc 4rpp 4wj8 4yj5 5x1w

(-) Related Entries Specified in the PDB File

5x1w