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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.65A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIAZOLE COMPOUND AND PMP COFACTOR.
 
Authors :  D. O. Somers
Date :  15 Feb 16  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Borthwick, N. Ancellin, S. M. Bertrand, R. P. Bingham, P. S. Carter, C. W. Chung, I. Churcher, N. Dodic, C. Fournier, P. L. Francis, A. Hobbs, C. Jamieson, S. D. Pickett, S. E. Smith, D. O. Somers, C. Spitzfaden, C. J. Suckling, R. J. Young
Structurally Diverse Mitochondrial Branched Chain Aminotransferase (Bcatm) Leads With Varying Binding Modes Identified By Fragment Screening.
J. Med. Chem. V. 59 2452 2016
PubMed-ID: 26938474  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01607

(-) 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 Taxid: 562
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    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, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
168C2Ligand/Ion5-METHYL-4-OXO-N-(1,3,4-THIADIAZOL-2-YL)-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-6-CARBOXAMIDE
2CL6Ligand/IonCHLORIDE ION
3EDO11Ligand/Ion1,2-ETHANEDIOL
4GOL5Ligand/IonGLYCEROL
5PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
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 , LEU A:266 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , HOH A:532 , HOH A:634 , HOH A:643binding site for residue PMP A 401
02AC2SOFTWAREPHE A:30 , PHE A:75 , LYS A:79 , TYR A:141 , VAL A:170 , TYR A:173 , LYS A:202 , ALA A:314 , HOH A:529 , HOH A:541 , HOH A:603 , HOH A:648 , HOH A:742 , HOH A:831 , HOH A:863 , VAL B:155binding site for residue 68C A 402
03AC3SOFTWARELYS A:79 , GLN A:316binding site for residue CL A 403
04AC4SOFTWAREARG A:102 , HOH A:755binding site for residue CL A 404
05AC5SOFTWAREARG A:92 , TRP A:94 , HOH A:826 , HOH A:828 , HOH A:899binding site for residue CL A 405
06AC6SOFTWARETYR A:246 , ARG A:306 , ARG A:344 , HOH A:606binding site for residue EDO A 406
07AC7SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , LEU A:162 , HOH A:524binding site for residue EDO A 407
08AC8SOFTWAREGLN A:11 , LEU A:12 , ASP A:187 , ALA A:189 , PHE A:190 , ARG A:220 , HOH A:504binding site for residue EDO A 408
09AC9SOFTWARELEU A:115 , GLU A:116 , GLU A:119 , HOH A:507 , HOH A:709 , HOH A:753 , HOH A:803binding site for residue EDO A 409
10AD1SOFTWAREGLY A:282 , GLU A:283 , PHE A:284 , HOH A:928 , HOH B:738binding site for residue EDO A 410
11AD2SOFTWAREGLN A:279 , VAL A:286 , GLU A:288 , HOH A:598 , HOH A:611 , HOH A:640 , HOH A:679binding site for residue EDO A 411
12AD3SOFTWAREARG A:106 , GLY A:196 , GLY A:197 , HOH A:704 , PHE B:190 , ILE B:191 , PRO B:209binding site for residue EDO A 412
13AD4SOFTWAREHIS A:249 , GLN A:295 , ASP B:85 , ARG B:89 , GLY B:355 , ILE B:356 , HOH B:594binding site for residue EDO A 413
14AD5SOFTWAREASP A:276 , MET A:277 , THR A:280 , GLU A:348 , ARG A:357 , HIS A:359 , HOH A:501 , HOH A:513binding site for residue GOL A 414
15AD6SOFTWARETRP A:94 , HOH A:515 , HOH A:788binding site for residue GOL A 415
16AD7SOFTWAREARG B:99 , ARG B:192 , LYS B:202 , 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:523 , HOH B:648 , HOH B:693binding site for residue PMP B 401
17AD8SOFTWAREVAL A:155 , PHE B:30 , PHE B:75 , LYS B:79 , TYR B:141 , TYR B:173 , LYS B:202 , ALA B:314 , HOH B:536 , HOH B:615 , HOH B:643 , HOH B:682 , HOH B:717 , HOH B:823 , HOH B:901binding site for residue 68C B 402
18AD9SOFTWARELYS B:79 , GLN B:316binding site for residue CL B 403
19AE1SOFTWAREHOH B:806 , HOH B:885binding site for residue CL B 404
20AE2SOFTWAREARG B:92 , TRP B:94 , HOH B:533 , HOH B:759binding site for residue CL B 405
21AE3SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:517 , HOH B:527binding site for residue EDO B 406
22AE4SOFTWAREGLU B:42 , ARG B:52 , LEU B:59 , THR B:60 , LEU B:162 , HOH B:550 , HOH B:722binding site for residue EDO B 407
23AE5SOFTWAREGLY B:282 , PHE B:284 , HOH B:567 , HOH B:746binding site for residue EDO B 408
24AE6SOFTWARELEU B:300 , GLU B:301 , ASN B:329 , LEU B:330 , HIS B:331 , HOH B:638 , HOH B:860binding site for residue GOL B 409
25AE7SOFTWARETRP B:94 , HOH B:521 , HOH B:533 , HOH B:618binding site for residue GOL B 410
26AE8SOFTWAREASP B:276 , MET B:277 , THR B:280 , GLU B:348 , HIS B:359 , HOH B:512 , HOH B:591 , HOH B:728 , HOH B:798binding site for residue GOL B 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I5X)

(-) 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 5I5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I5X)

(-) Exons   (0, 0)

(no "Exon" information available for 5I5X)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               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.hhhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i5x A   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357        
                                               23|                                                                                                                                                174|                                                                                                                                                                                            
                                                27                                                                                                                                                 177                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               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
                 5i5x B  -2 SHMASSSFKAADLQLEMTQKPHKKPGLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                     7        17     || 31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
                                                    23|                                                                                                                                                                                                                                                                                                                                                 
                                                     28
   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 5I5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I5X)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  5i5x
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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 5bwx 5cr5 5hne 5i5s 5i5t 5i5u 5i5v 5i5w 5i5y 5i60

(-) Related Entries Specified in the PDB File

5i5s 5i5t 5i5u 5i5v 5i5w 5i5y 5i60