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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 2.20A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE FRAGMENT AND AN INTERNAL ALDIMINE LINKED PLP.
 
Authors :  D. O. Somers
Date :  08 Jun 15  (Deposition) - 01 Jul 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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
    Fragment: RESIDUES 28-392
    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, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
14VS2Ligand/Ion5-ETHYL-2-METHYL-7-OXO-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2CL3Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , ARG A:192 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , MET A:241 , ASN A:242 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , HOH A:563 , HOH A:574 , HOH A:593 , HOH A:668binding site for residue PLP A 401
02AC2SOFTWARETYR A:141 , ARG A:143 , TYR A:173 , PHE A:174 , THR A:240 , MET A:241 , ALA A:314 , CYS A:315 , HOH A:646 , HOH A:658 , HOH A:664 , VAL B:155binding site for residue 4VS A 402
03AC3SOFTWAREARG A:92 , TRP A:94 , HOH A:687 , HOH A:717binding site for residue CL A 404
04AC4SOFTWARETYR A:246 , LEU A:341 , ARG A:344 , HOH A:573binding site for residue EDO A 405
05AC5SOFTWAREASP A:276 , THR A:280 , ARG A:357 , HIS A:359 , TRP A:361binding site for residue EDO A 406
06AC6SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , LEU A:162 , HOH A:630binding site for residue EDO A 407
07AC7SOFTWAREASP A:276 , VAL A:286 , GLU A:288 , HOH A:537 , HOH A:683binding site for residue GOL A 408
08AC8SOFTWAREVAL A:155 , TYR B:141 , TYR B:173 , THR B:240 , MET B:241 , GLY B:312 , ALA B:314 , CYS B:315 , HOH B:598 , HOH B:665binding site for residue 4VS B 402
09AC9SOFTWAREHOH B:775binding site for residue CL B 403
10AD1SOFTWAREASP B:276 , MET B:277 , THR B:280 , GLU B:348 , HIS B:359 , HOH B:526binding site for residue EDO B 404
11AD2SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344binding site for residue EDO B 405
12AD3SOFTWAREGLU B:42 , LEU B:59 , THR B:60binding site for residue EDO B 406
13AD4SOFTWARELEU 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 , MET B:241 , ASN B:242 , LEU B:266 , GLY B:268 , VAL B:269 , VAL B:270 , GLY B:312 , THR B:313 , HOH B:540 , HOH B:550 , HOH B:591 , HOH B:659binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

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

(-) 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 5BWT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWT)

(-) 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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               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..eeeeeee......eeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bwt A   3 SSFKAADLQLEMTQKPHKKPGPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  ||   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
                                                                                                                                                                                                      175|                                                                                                                                                                                          
                                                                                                                                                                                                       179                                                                                                                                                                                          


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..eeeeeee......eeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwt B   2 SSSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    11        21 ||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|      188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
                                                23|                                                                                                                                                174|                                                                                                                                                                                          
                                                 27                                                                                                                                                 179
   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 5BWT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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

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