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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.94A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIENOPYRIMIDINE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
 
Authors :  D. O. Somers
Date :  15 Feb 16  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
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  (6, 24)

Asymmetric/Biological Unit (6, 24)
No.NameCountTypeFull Name
168A2Ligand/Ion3,5-DIMETHYL-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-6-CARBOXYLIC ACID
2CL2Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4EDO14Ligand/Ion1,2-ETHANEDIOL
5GOL2Ligand/IonGLYCEROL
6PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , ARG A:192 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , ASN A:242 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , EDO A:404 , EDO A:405 , HOH A:564 , HOH A:602 , HOH A:629binding site for residue PLP A 401
02AC2SOFTWAREPHE A:30 , LYS A:79 , TYR A:141 , GLY A:171 , TYR A:173 , ALA A:314 , EDO A:404 , HOH A:643 , HOH A:741 , HOH A:755binding site for residue 68A A 402
03AC3SOFTWAREHOH A:721 , HOH A:761binding site for residue CL A 403
04AC4SOFTWAREARG A:143 , LYS A:202 , PLP A:401 , 68A A:402 , EDO A:405 , HOH A:541 , TYR B:70binding site for residue EDO A 404
05AC5SOFTWARETHR A:240 , THR A:313 , ALA A:314 , PLP A:401 , EDO A:404 , HOH A:707binding site for residue EDO A 405
06AC6SOFTWARETYR A:70 , ARG B:143 , LYS B:202 , PLP B:401 , 68A B:402 , EDO B:404 , HOH B:578binding site for residue EDO A 406
07AC7SOFTWARETYR A:246 , ARG A:306 , LEU A:341 , ARG A:344 , HOH A:547binding site for residue EDO A 407
08AC8SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , HOH A:519 , HOH A:624binding site for residue EDO A 408
09AC9SOFTWARELEU A:261 , HOH A:508 , ALA B:358binding site for residue EDO A 409
10AD1SOFTWAREHIS A:249 , ASP B:85 , ARG B:89 , TYR B:354 , ILE B:356 , HOH B:538binding site for residue EDO A 410
11AD2SOFTWAREARG A:99 , ARG A:102 , PRO A:267 , GLY A:268 , HOH A:596 , HOH A:740binding site for residue EDO A 411
12AD3SOFTWAREGLU A:116 , GLU A:119 , HOH A:657binding site for residue EDO A 412
13AD4SOFTWARELEU A:261 , ASN A:262 , HOH A:560binding site for residue EDO A 413
14AD5SOFTWARETHR A:280 , HIS A:359 , TRP A:361 , HOH A:631binding site for residue DMS A 414
15AD6SOFTWAREHOH A:516 , HOH A:671 , HOH A:713binding site for residue GOL A 415
16AD7SOFTWAREEDO A:406 , PHE B:30 , LYS B:79 , TYR B:141 , GLY B:171 , TYR B:173 , ALA B:314 , HOH B:501 , HOH B:797binding site for residue 68A B 402
17AD8SOFTWAREHOH B:728 , HOH B:826binding site for residue CL B 403
18AD9SOFTWAREEDO A:406 , THR B:240 , ALA B:314 , PLP B:401 , HOH B:517binding site for residue EDO B 404
19AE1SOFTWARETYR B:246 , ARG B:306 , ARG B:344 , HOH B:560binding site for residue EDO B 405
20AE2SOFTWAREGLU B:42 , ARG B:52 , THR B:60 , LEU B:162 , HOH B:639binding site for residue EDO B 406
21AE3SOFTWAREPHE B:284 , HOH B:564 , HOH B:685binding site for residue EDO B 407
22AE4SOFTWAREASP B:276 , THR B:280 , HIS B:359 , TRP B:361binding site for residue DMS B 408
23AE5SOFTWARETRP B:94 , HOH B:531 , HOH B:562 , HOH B:689binding site for residue GOL B 409
24AE6SOFTWAREEDO A:406 , LEU 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 , EDO B:404 , HOH B:525 , HOH B:577 , HOH B:612binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I5V)

(-) 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 5I5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I5V)

(-) Exons   (0, 0)

(no "Exon" information available for 5I5V)

(-) 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: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...........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
                 5i5v A   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                                                                                                                                                                                                                                                                                                                                                  


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...........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
                 5i5v 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 5I5V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I5V)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 5i5w 5i5x 5i5y 5i60

(-) Related Entries Specified in the PDB File

5i5s 5i5t 5i5u 5i5w 5i5x 5i5y 5i60