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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 2.06A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BENZISOXAZOLE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
 
Authors :  D. Somers
Date :  15 Feb 16  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
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 Plasmid: PET-28A
    Expression System Taxid: 562
    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  (6, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO10Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5NVU2Ligand/Ion2-(1,2-BENZOXAZOL-3-YL)ETHANOIC ACID
6PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
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 , NVU A:402 , HOH A:548 , HOH A:569 , HOH A:605binding site for residue PLP A 401
02AC2SOFTWAREPHE A:30 , PHE A:75 , LYS A:202 , THR A:240 , THR A:313 , ALA A:314 , PLP A:401 , HOH A:513 , HOH A:527 , TYR B:70 , LEU B:153 , VAL B:155binding site for residue NVU A 402
03AC3SOFTWAREARG A:92 , TRP A:94 , EDO A:410 , HOH A:751binding site for residue CL A 403
04AC4SOFTWARETYR A:246 , GLU A:340 , LEU A:341 , ARG A:344 , HOH A:539binding site for residue EDO A 405
05AC5SOFTWAREASP A:276 , MET A:277 , THR A:280 , HIS A:359 , HOH A:607binding site for residue EDO A 406
06AC6SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , HOH A:580binding site for residue EDO A 407
07AC7SOFTWARELEU A:261 , ASN A:262 , HOH A:510 , HOH B:768binding site for residue EDO A 408
08AC8SOFTWARELEU A:261 , ASN A:262 , GLY A:263binding site for residue EDO A 409
09AC9SOFTWARETRP A:94 , GLU A:360 , CL A:403binding site for residue EDO A 410
10AD1SOFTWAREGLY A:282 , PHE A:284 , ARG A:285 , HOH A:553 , HOH B:530 , HOH B:531binding site for residue GOL A 411
11AD2SOFTWARETYR A:70 , LEU A:153 , VAL A:155 , PHE B:30 , PHE B:75 , LYS B:202 , THR B:240 , THR B:313 , ALA B:314 , PLP B:401 , HOH B:535 , HOH B:543binding site for residue NVU B 402
12AD3SOFTWAREARG B:92 , TRP B:94 , HOH B:682 , HOH B:694 , HOH B:735binding site for residue CL B 403
13AD4SOFTWAREHOH B:800binding site for residue CL B 404
14AD5SOFTWAREASP B:276 , MET B:277 , THR B:280 , GLU B:348 , HIS B:359 , HOH B:504binding site for residue EDO B 405
15AD6SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:540binding site for residue EDO B 406
16AD7SOFTWAREARG A:106 , GLY A:196 , GLY A:197 , PHE B:190 , ILE B:191 , HOH B:528binding site for residue EDO B 407
17AD8SOFTWAREHOH B:525 , HOH B:694binding site for residue EDO B 408
18AD9SOFTWAREGLU B:42 , ARG B:52 , LEU B:59 , THR B:60 , HOH B:510 , HOH B:666binding site for residue DMS B 409
19AE1SOFTWARELEU 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 , NVU B:402 , HOH B:542 , HOH B:587 , HOH B:614binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I5S)

(-) 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 5I5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I5S)

(-) Exons   (0, 0)

(no "Exon" information available for 5I5S)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               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
                 5i5s A   3 SSFKAADLQLEMTQKPHKKPGEPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 
                                               23|                                                                                                                                                                                                                                                                                                                                                   
                                                26                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               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
                 5i5s B   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359      
                                               23|                                                                                                                                               173|                                                                                                                                                                                           
                                                27                                                                                                                                                178
   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 5I5S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I5S)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60

(-) Related Entries Specified in the PDB File

5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60