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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A 2-ARYL BENZIMIDAZOLE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR
 
Authors :  D. O. Somers
Date :  18 Jan 16  (Deposition) - 04 May 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Deng, J. Zhou, F. Sundersingh, J. A. Messer, D. O. Somers, M. Ajakane C. C. Arico-Muendel, A. Beljean, S. L. Belyanskaya, R. Bingham, E. Blazensky, A. B. Boullay, E. Boursier, J. Chai, P. Carter, C. W. Chung, A. Daugan, Y. Ding, K. Herry, C. Hobbs, E. Humphries, C. Kollmann, V. L. Nguyen, E. Nicodeme, S. E. Smith, N. Dodic, N. Ancellin
Discovery And Optimization Of Potent, Selective, And In Viv Efficacious 2-Aryl Benzimidazole Bcatm Inhibitors.
Acs Med. Chem. Lett. V. 7 379 2016
PubMed-ID: 27096045  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00389

(-) 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 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, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3EL22Ligand/Ion1-[(1R,3S)-3-{[(5-BROMOTHIOPHEN-2-YL)CARBONYL]AMINO}CYCLOHEXYL]-N-METHYL-2-(PYRIDIN-2-YL)-1H-BENZIMIDAZOLE-5-CARBOXAMIDE
4GOL1Ligand/IonGLYCEROL
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
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 , EL2 A:402 , HOH A:527 , HOH A:628 , HOH A:639binding site for residue PLP A 401
02AC2SOFTWAREPHE A:30 , LYS A:79 , GLY A:171 , TYR A:173 , VAL A:182 , LYS A:202 , GLN A:224 , VAL A:238 , GLY A:239 , THR A:240 , MET A:241 , ALA A:314 , PLP A:401 , HOH A:523 , HOH A:525 , HOH A:611binding site for residue EL2 A 402
03AC3SOFTWAREARG A:92 , TRP A:94 , HOH A:655 , HOH A:805binding site for residue CL A 403
04AC4SOFTWARELEU A:261 , GLY A:263 , HOH A:708binding site for residue EDO A 404
05AC5SOFTWARETYR A:246 , ARG A:306 , GLU A:340 , ARG A:344 , HOH A:564 , HOH A:627binding site for residue EDO A 405
06AC6SOFTWAREMET A:277 , THR A:280 , HIS A:359 , TRP A:361 , HOH A:701binding site for residue EDO A 406
07AC7SOFTWAREGLN A:11 , LEU A:12 , ASP A:187 , ALA A:189 , PHE A:190 , ARG A:220binding site for residue EDO A 407
08AC8SOFTWAREGLU A:42 , LEU A:59 , THR A:60binding site for residue EDO A 408
09AC9SOFTWAREPRO A:260 , LEU A:261 , ASN A:262 , HOH A:521 , ALA B:358binding site for residue EDO A 409
10AD1SOFTWAREARG A:106 , GLY A:196 , GLY A:197 , HOH A:503 , ILE B:191binding site for residue EDO A 410
11AD2SOFTWAREPHE B:30 , LYS B:79 , GLY B:171 , TYR B:173 , VAL B:182 , LYS B:202 , GLN B:224 , VAL B:238 , GLY B:239 , THR B:240 , MET B:241 , ALA B:314 , CYS B:318 , PLP B:401 , HOH B:517 , HOH B:577 , HOH B:650binding site for residue EL2 B 402
12AD3SOFTWAREARG B:92 , TRP B:94 , HOH B:670 , HOH B:798binding site for residue CL B 403
13AD4SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:576binding site for residue EDO B 404
14AD5SOFTWAREASP B:276 , MET B:277 , THR B:280 , GLU B:348 , HIS B:359 , HOH B:502binding site for residue EDO B 405
15AD6SOFTWAREGLU B:42 , ARG B:52 , LEU B:59 , THR B:60 , LEU B:162 , HOH B:503 , HOH B:647binding site for residue GOL B 406
16AD7SOFTWARELEU 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 , EL2 B:402 , HOH B:532 , HOH B:668binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

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

(-) 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 5HNE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HNE)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               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
                 5hne A   3 SSFKAADLQLEMTQKPHKKPPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
                                              22|                                                                                                                                                                                                                                                                                                                                                  
                                               27                                                                                                                                                                                                                                                                                                                                                  


Chain B 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..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hne B   3 SSFKAADLQLEMTQKPHKKPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22|       37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357        
                                              22|                                                                                                                                                                                                                                                                                                                                                 
                                               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 5HNE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 5i5s 5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60

(-) Related Entries Specified in the PDB File

5cr5 5CR5 CONTAINS THE SAME PROTEIN COMPLEXED WITH A BIPHENYL PYRROLIDINE ETHER COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.