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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.70A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A 4-CHLORO-2-FLUORO SUBSTITUTED 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 :  1.70
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  (6, 26)

Asymmetric/Biological Unit (6, 26)
No.NameCountTypeFull Name
14W42Ligand/Ion5-BUTYL-2-[(4-CHLORO-2-FLUOROBENZYL)AMINO]-7-OXO-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2CL2Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4EDO17Ligand/Ion1,2-ETHANEDIOL
5GOL2Ligand/IonGLYCEROL
6PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , ARG A:192 , 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 , 4W4 A:402 , HOH A:568 , HOH A:669 , HOH A:693binding site for residue PLP A 401
02AC2SOFTWARETYR A:141 , ARG A:143 , VAL A:182 , LYS A:202 , GLN A:224 , VAL A:238 , GLY A:239 , THR A:240 , MET A:241 , GLY A:312 , ALA A:314 , CYS A:315 , CYS A:318 , PLP A:401 , EDO A:403 , HOH A:630 , HOH A:674 , LEU B:153 , VAL B:155binding site for residue 4W4 A 402
03AC3SOFTWARECYS A:315 , 4W4 A:402 , HOH A:668binding site for residue EDO A 403
04AC4SOFTWAREASP A:276 , THR A:280 , GLU A:348 , ARG A:357 , HIS A:359binding site for residue EDO A 404
05AC5SOFTWAREARG A:102 , PRO A:267 , HOH A:652binding site for residue EDO A 405
06AC6SOFTWARETYR A:246 , ARG A:306 , ARG A:344 , HOH A:575binding site for residue EDO A 406
07AC7SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , HOH A:594binding site for residue EDO A 407
08AC8SOFTWAREGLN A:234 , ASN A:262 , THR A:290 , HOH A:663binding site for residue EDO A 408
09AC9SOFTWARETRP A:94 , HOH A:736binding site for residue EDO A 409
10AD1SOFTWAREARG A:106 , GLY A:196 , GLY A:197 , HOH A:619 , ILE B:191 , PRO B:209binding site for residue EDO A 410
11AD2SOFTWAREGLN A:16 , TRP A:194 , TYR A:229 , GLY A:230 , HOH A:512 , HOH A:534 , HOH A:617 , TRP B:194binding site for residue EDO A 411
12AD3SOFTWAREGLU A:216 , HOH A:692binding site for residue EDO A 412
13AD4SOFTWARETRP A:94 , ASP A:98 , LYS A:114binding site for residue EDO A 413
14AD5SOFTWAREARG A:102 , ASN A:200 , TYR A:201 , CL A:416 , HOH A:604 , HOH A:694 , HOH A:717binding site for residue EDO A 414
15AD6SOFTWAREASN A:200 , LEU A:261 , ASN A:262 , HOH A:513 , HOH A:717binding site for residue EDO A 415
16AD7SOFTWAREEDO A:414 , HOH A:513binding site for residue CL A 416
17AD8SOFTWAREPRO A:260 , LEU A:261 , HOH A:520 , HOH A:660binding site for residue GOL A 417
18AD9SOFTWAREVAL A:155 , TYR B:141 , ARG B:143 , VAL B:182 , LYS B:202 , GLN B:224 , VAL B:238 , GLY B:239 , THR B:240 , MET B:241 , GLY B:312 , ALA B:314 , CYS B:315 , CYS B:318 , PLP B:401 , EDO B:404 , HOH B:640 , HOH B:681binding site for residue 4W4 B 402
19AE1SOFTWAREMET B:40 , GLU B:42 , LEU B:59 , THR B:60 , HOH B:595binding site for residue DMS B 403
20AE2SOFTWAREPHE B:30 , TYR B:173 , 4W4 B:402 , HOH B:766binding site for residue EDO B 404
21AE3SOFTWAREASP B:276 , THR B:280 , GLU B:348 , HIS B:359 , TRP B:361 , HOH B:520binding site for residue EDO B 405
22AE4SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:652binding site for residue EDO B 406
23AE5SOFTWAREGLU B:336 , ASN B:337 , HOH B:551 , HOH B:592binding site for residue EDO B 407
24AE6SOFTWAREHOH B:539 , HOH B:674 , HOH B:718binding site for residue GOL B 409
25AE7SOFTWARELEU 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 , 4W4 B:402 , HOH B:575 , HOH B:588 , HOH B:659binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

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

(-) 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 5BWX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWX)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               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
                 5bwx A   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165     ||182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
                                               23|                                                                                                                                             171|                                                                                                                                                                                          
                                                27                                                                                                                                              179                                                                                                                                                                                          


Chain B 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...hhhhh...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
                 5bwx B   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
                                               23|                                                                                                                                                                                                                                                                                                                                                  
                                                27
   Legend:   → Mismatch (orange background)
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    → 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 5BWX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  5bwx
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  BCAT2_HUMAN | O15382
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  2.6.1.42
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5bwr 5bwt 5bwu 5bwv 5bww