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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.86A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
 
Authors :  D. O. Somers
Date :  08 Jun 15  (Deposition) - 01 Jul 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Bertrand, N. Ancellin, B. Beaufils, R. P. Bingham, J. A. Borthwick, A. B. Boullay, E. Boursier, P. S. Carter, C. W. Chung, I. Churcher, N. Dodic, M. H. Fouchet, C. Fournier, P. L. Francis, L. A. Gummer, K. Herry, A. Hobbs, C. I. Hobbs, P. Homes, C. Jamieson, E. Nicodeme, S. D. Pickett, I. H. Reid, G. L. Simpson, L. A. Sloan, S. E. Smith, D. O. Somers, C. Spitzfaden, C. J. Suckling, K. Valko, Y. Washio, R. J. Young
The Discovery Of In Vivo Active Mitochondrial Branched-Chai Aminotransferase (Bcatm) Inhibitors By Hybridizing Fragment And Hts Hits.
J. Med. Chem. V. 58 7140 2015
PubMed-ID: 26090771  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00313

(-) Compounds

Molecule 1 - BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 2.6.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 38-392
    Gene: BCAT2, BCATM, BCT2, ECA40
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCAT(M),PLACENTAL PROTEIN 18,PP18

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
17752Ligand/Ion2-[(4-CHLOROBENZYL)AMINO]-7-OXO-5-PROPYL-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2CL4Ligand/IonCHLORIDE ION
3EDO16Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , ASN A:242 , LEU A:266 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , HOH A:522 , HOH A:574 , HOH A:640 , HOH A:758binding site for residue PLP A 401
02AC2SOFTWARETYR A:141 , ARG A:143 , TYR A:173 , VAL A:182 , GLN A:224 , VAL A:238 , THR A:240 , MET A:241 , GLY A:312 , ALA A:314 , CYS A:315 , CYS A:318 , VAL A:320 , EDO A:405 , HOH A:659 , HOH A:710 , VAL B:155binding site for residue 775 A 402
03AC3SOFTWAREARG A:92 , TRP A:94 , EDO A:415 , HOH A:672 , HOH A:791 , HOH A:809binding site for residue CL A 404
04AC4SOFTWARETYR A:173 , GLN A:224 , 775 A:402 , HOH A:506 , HOH A:518 , HOH A:739 , VAL B:155binding site for residue EDO A 405
05AC5SOFTWAREVAL A:155 , HOH A:512 , HOH A:536 , HOH A:687 , TYR B:173 , GLN B:224 , THR B:240 , 775 B:402binding site for residue EDO A 406
06AC6SOFTWAREHIS A:359 , TRP A:361 , HOH A:527binding site for residue EDO A 407
07AC7SOFTWAREARG A:99 , ARG A:102 , PRO A:267 , GLY A:268 , VAL A:269 , HOH A:699 , HOH A:744binding site for residue EDO A 408
08AC8SOFTWARETYR A:246 , ARG A:306 , ARG A:344 , HOH A:708binding site for residue EDO A 409
09AC9SOFTWAREGLN A:234 , ASN A:262 , HOH A:554 , HOH A:734binding site for residue EDO A 410
10AD1SOFTWARETYR A:229 , GLY A:230 , HOH A:505 , HOH A:560 , HOH A:580 , TRP B:194binding site for residue EDO A 411
11AD2SOFTWAREGLY A:83 , LYS A:84 , ASP A:85 , ARG A:89 , GLY A:355binding site for residue EDO A 412
12AD3SOFTWAREHIS A:249 , GLN A:295 , GLY B:83 , LYS B:84 , ASP B:85 , ILE B:356 , HOH B:536 , HOH B:585binding site for residue EDO A 413
13AD4SOFTWAREGLU A:116 , GLU A:119 , HOH A:557 , HOH A:558binding site for residue EDO A 414
14AD5SOFTWARETRP A:94 , CL A:404 , HOH A:552 , HOH A:672 , HOH A:791binding site for residue EDO A 415
15AD6SOFTWAREGLN A:11 , LEU A:12 , ASP A:187 , PHE A:190 , GLU A:216 , ARG A:220binding site for residue EDO A 416
16AD7SOFTWAREASN A:337 , GLY A:338 , HOH A:592 , HOH A:693 , HOH A:777 , ASN B:329binding site for residue GOL A 417
17AD8SOFTWAREVAL A:155 , EDO A:406 , PHE B:75 , TYR B:141 , ARG B:143 , TYR B:173 , VAL B:182 , GLN B:224 , VAL B:238 , THR B:240 , MET B:241 , GLY B:312 , ALA B:314 , CYS B:315 , CYS B:318 , VAL B:320 , HOH B:506 , HOH B:656binding site for residue 775 B 402
18AD9SOFTWAREHOH B:903binding site for residue CL B 403
19AE1SOFTWAREARG B:92 , TRP B:94 , HOH B:725 , HOH B:793 , HOH B:970binding site for residue CL B 404
20AE2SOFTWAREASP B:276 , THR B:280 , GLU B:348 , HIS B:359 , TRP B:361 , HOH B:583binding site for residue EDO B 405
21AE3SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:642 , HOH B:660binding site for residue EDO B 406
22AE4SOFTWAREGLU B:42 , ARG B:52 , LEU B:59 , THR B:60 , LEU B:162 , HOH B:547 , HOH B:754binding site for residue EDO B 407
23AE5SOFTWAREGLU B:116 , GLU B:119 , LYS B:326 , HOH B:568binding site for residue EDO B 408
24AE6SOFTWARELEU B:74 , PHE B:75 , ARG B:99 , SER B:103 , ARG B:192 , TYR B:201 , LEU B:203 , TYR B:207 , GLU B:237 , THR B:240 , ASN B:242 , LEU B:266 , GLY B:268 , VAL B:269 , VAL B:270 , GLY B:312 , THR B:313 , HOH B:548 , HOH B:570 , HOH B:615 , HOH B:747binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:338 -Pro A:339
2Gly B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWV)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee....................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee.......eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwv A   3 SSFKAADLQLEMTQKPHKKPPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22|       36        46        56        66        76        86        96       106       116       126       136       146       156       166      |180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
                                              22|                                                                                                                                               173|                                                                                                                                                                                           
                                               27                                                                                                                                                178                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee.....................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee........eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwv B   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
                                               23|                                                                                                                                               173|                                                                                                                                                                                            
                                                27                                                                                                                                                177
   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 5BWV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  5bwv
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  BCAT2_HUMAN | O15382
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  2.6.1.42
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 Related Entries

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UniProtKB/Swiss-Prot
        BCAT2_HUMAN | O15382: 1ekf 1ekp 1ekv 1kt8 1kta 2a1h 2hdk 2hg8 2hgw 2hgx 2hhf 5bwr 5bwt 5bwu 5bww 5bwx 5cr5 5hne 5i5s 5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60

(-) Related Entries Specified in the PDB File

5bwr 5bwt 5bwu