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(-) Description

Title :  CRYSTAL STRUCTURE OF A MYCOBACTERIAL PROTEIN
 
Authors :  W. J. Li, L. J. Bi
Date :  12 Aug 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mycobacterium Smegmatis, Ligase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Li, S. Gu, J. Fleming, L. Bi
Crystal Structure Of Fadd32, An Enzyme Essential For Mycoli Acid Biosynthesis In Mycobacteria.
Sci Rep V. 5 15493 2015
PubMed-ID: 26628098  |  Reference-DOI: 10.1038/SREP15493

(-) Compounds

Molecule 1 - ACYL-COA SYNTHASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FADD32, MSMEG_6393, MSMEI_6225
    Organism Scientific: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / MC(2)155)
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155
    Synonym: FATTY-ACID-COA LIGASE FADD32
 
Molecule 2 - UBIQUITIN-LIKE PROTEIN SMT3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-94
    Gene: SMT3, YDR510W, D9719.15
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREATP A:702 , HOH A:827 , HOH A:835 , HOH A:921 , HOH A:926binding site for residue MG A 701
2AC2SOFTWARETHR A:187 , SER A:188 , GLY A:189 , SER A:190 , THR A:191 , ARG A:192 , SER A:314 , GLU A:315 , PRO A:316 , SER A:342 , GLY A:344 , LEU A:345 , ALA A:346 , ASP A:469 , ILE A:480 , ARG A:483 , MG A:701 , HOH A:827 , HOH A:835 , HOH A:921 , HOH A:924 , HOH A:926 , HOH A:973 , HOH A:988 , HOH A:1060 , HOH A:1122binding site for residue ATP A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D6J)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:451 -Pro A:452
2His A:560 -Lys A:561
3Asp A:613 -Gly A:614

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D6J)

(-) Exons   (0, 0)

(no "Exon" information available for 5D6J)

(-) 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:630
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..ee......hhhhhhhhhhhhh...eeeeeee.......eeeeeehhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhh..........eeeeee.........eeeeehhhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh.........eee.hhhhhhhhhhhh...............eeee.....hhhhhhhhhhhhhhhh.hhh.eeeeee.hhhh.eeee........eeeeehhhhhh............eeeee...ee...eeeeeee....ee......eeeeeee.........hhhhhhhhhh.....................eeeeeeeeee..eeeeeee.hhheee..eeehhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhh.........eeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeee.............hhhhhhhhhh.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d6j A   1 MPFHNPFIKDGQIKFPDGSSIVAHVERWAKVRGDKLAYRFLDFSTERDGVPRDLTWAQFSARNRAVAARLQQVTQPGDRVAILCPQNLDYLVAFFGALYAGRIAVPLFDPSEPGHVGRLHAVLDNCHPSAILTTTEAAEGVRKFFRTRPANQRPRVIAVDAVPDDVASTWVNPDEPDETTIAYLQYTSGSTRIPTGVQITHLNLATNVVQVIEALEGEEGDRGLSWLPFFHDMGLITALLAPMIGHYFTFMTPAAFVRRPERWIRELARKEGDTGGTISVAPNFAFDHAAARGVPKPGSPPLDLSNVKAVLNGSEPISAATVRRFNEAFGPFGFPPKAIKPSYGLAEATLFVSTTPSAEEPKIITVDRDQLNSGRIVEVDADSPKAVAQASAGKVGIAEWAVIVDAESATELPDGQVGEIWISGQNMGTGYWGKPEESVATFQNILKSRTNPSHAEGATDDATWVRTGDYGAFYDGDLYITGRVKDLVIIDGRNHYPQDLEYSAQEASKAIRTGYVAAFSVPANQLPDEVFENAHSGIKRDPDDTSEQLVIVAERAPGAHKLDIGPITDDIRAAIAVRHGVTVRDVLLTAAGAIPRTSSGKIGRRACRAAYLDGSLRAGKVANDFPDATD 630
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....hhhhhhhhhhhh..hhh.eeeee..ee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5d6j B  21 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE  94
                                    30        40        50        60        70        80        90
   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 5D6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D6J)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:451 - Pro A:452   [ RasMol ]  
    Asp A:613 - Gly A:614   [ RasMol ]  
    His A:560 - Lys A:561   [ RasMol ]  
 

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  SMT3_YEAST | Q12306
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SMT3_YEAST | Q12306: 1euv 1l2n 2eke 3pge 3qht 3tix 3uf8 3uqa 3uqb 3v60 3v61 3v62 3vaw 4fn2 4g50 4ggq 4giv 5jne 5klx
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        A0R618_MYCS2 | A0R618: 5d6n 5ey8 5icr

(-) Related Entries Specified in the PDB File

5d6n