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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.61A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIPHENYL PYRROLIDINE ETHER COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
 
Authors :  D. O. Somers
Date :  22 Jul 15  (Deposition) - 12 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Deng, J. Zhou, F. S. Sundersingh, J. Summerfield, D. Somers, J. A. Messer, A. L. Satz, N. Ancellin, C. C. Arico-Muendel, K. L. Sargent Bedard, A. Beljean, S. L. Belyanskaya, R. Bingham, S. E. Smith, E. Boursier, P. Carter, P. A. Centrella, M. A. Clark, C. W. Chung, C. P. Davie, J. L. Delorey, Y. Ding, G. J. Franklin, L. C. Grady, K. Herry, C. Hobbs, C. S. Kollmann, B. A. Morgan, L. J. Pothier Kaushansky, Q. Zhou
Discovery, Sar, And X-Ray Binding Mode Study Of Bcatm Inhibitors From A Novel Dna-Encoded Library.
Acs Med. Chem. Lett. V. 6 919 2015
PubMed-ID: 26288694  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00179

(-) 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, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO6Ligand/Ion1,2-ETHANEDIOL
4EL12Ligand/Ion3-({(3R)-1-[(5-BROMOTHIOPHEN-2-YL)CARBONYL]PYRROLIDIN-3-YL}OXY)-N-METHYL-2'-[(METHYLSULFONYL)AMINO]BIPHENYL-4-CARBOXAMIDE
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
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 , EL1 A:402 , HOH A:548 , HOH A:662 , HOH A:718binding site for residue PLP A 401
02AC2SOFTWAREPHE A:30 , PHE A:75 , ARG A:143 , TYR A:173 , VAL A:182 , GLN A:224 , VAL A:238 , GLY A:239 , THR A:240 , MET A:241 , GLY A:312 , THR A:313 , ALA A:314 , CYS A:318 , PLP A:401 , HOH A:522 , HOH A:612 , TYR B:70binding site for residue EL1 A 402
03AC3SOFTWARELYS A:79 , GLN A:316 , HOH A:654binding site for residue CL A 403
04AC4SOFTWARETYR A:246 , ARG A:306 , ARG A:344 , HOH A:519 , HOH A:568binding site for residue EDO A 404
05AC5SOFTWAREGLN A:234 , ASN A:262 , THR A:290 , HOH A:524 , HOH A:566binding site for residue EDO A 405
06AC6SOFTWAREILE A:191 , TRP A:194 , TYR A:229 , GLY A:230 , HOH A:529 , HOH A:601 , HOH A:637 , TRP B:194binding site for residue EDO A 406
07AC7SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , HOH A:647binding site for residue EDO A 407
08AC8SOFTWARELEU A:261 , ASN A:262 , HOH A:809 , ALA B:358 , HIS B:359binding site for residue EDO A 408
09AC9SOFTWARETYR A:70 , PHE B:30 , ARG B:143 , TYR B:173 , VAL B:182 , GLN B:224 , VAL B:238 , GLY B:239 , THR B:240 , MET B:241 , GLY B:312 , THR B:313 , ALA B:314 , CYS B:318 , PLP B:401 , HOH B:514 , HOH B:529binding site for residue EL1 B 402
10AD1SOFTWARELYS B:79 , GLN B:316binding site for residue CL B 403
11AD2SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344binding site for residue EDO B 404
12AD3SOFTWAREGLU B:42 , LEU B:59 , THR B:60 , HOH B:684binding site for residue DMS B 405
13AD4SOFTWARELEU B:74 , PHE B:75 , ARG B:99 , SER B:103 , 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 , EL1 B:402 , HOH B:502 , HOH B:519 , HOH B:599 , HOH B:721binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CR5)

(-) 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 5CR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CR5)

(-) Exons   (0, 0)

(no "Exon" information available for 5CR5)

(-) 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
                 5cr5 A   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                                                                                                                                                                                                                                                                                                                                                 


Chain B 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...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
                 5cr5 B   3 SSFKAADLQLEMTQKPHKKPGLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 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         
                                               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 5CR5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CR5)

(-) 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 5bwt 5bwu 5bwv 5bww 5bwx 5hne 5i5s 5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60

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