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(-) Description

Title :  STRUCTURE OF MTB LPD BOUND TO SL827
 
Authors :  C. D. Lima
Date :  07 Aug 13  (Deposition) - 27 Nov 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Oxidoreductase, Flavoprotein, Glycolysis, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bryk, N. Arango, C. Maksymiuk, A. Balakrishnan, Y. T. Wu, C. H. Wong, T. Masquelin, P. Hipskind, C. D. Lima, C. Nathan
Lipoamide Channel-Binding Sulfonamides Selectively Inhibit Mycobacterial Lipoamide Dehydrogenase.
Biochemistry V. 52 9375 2013
PubMed-ID: 24251446  |  Reference-DOI: 10.1021/BI401077F

(-) Compounds

Molecule 1 - DIHYDROLIPOYL DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.8.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21 (DE3) CODON PLUS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LPD, LPD RV0462, LPDC, MT0478, MTV038.06, RV0462
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: 1773
    Synonym: LPD, COMPONENT OF PEROXYNITRITE REDUCTASE/PEROXIDASE COMPLEX, COMPONENT OF PNR/P, DIHYDROLIPOAMIDE DEHYDROGENASE, E3 COMPONENT OF ALPHA-KETOACID DEHYDROGENASE COMPLEXES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2M524Ligand/IonN~2~-[(2-AMINO-5-BROMOPYRIDIN-3-YL)SULFONYL]-N-(4-METHOXYPHENYL)-N~2~-METHYLGLYCINAMIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2M522Ligand/IonN~2~-[(2-AMINO-5-BROMOPYRIDIN-3-YL)SULFONYL]-N-(4-METHOXYPHENYL)-N~2~-METHYLGLYCINAMIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2M522Ligand/IonN~2~-[(2-AMINO-5-BROMOPYRIDIN-3-YL)SULFONYL]-N-(4-METHOXYPHENYL)-N~2~-METHYLGLYCINAMIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:9 , GLY A:10 , GLY A:12 , PRO A:13 , GLY A:14 , VAL A:32 , GLU A:33 , PRO A:34 , TYR A:36 , GLY A:39 , VAL A:40 , CYS A:41 , GLY A:45 , CYS A:46 , LYS A:50 , TYR A:112 , GLY A:113 , ALA A:141 , THR A:142 , GLY A:143 , TYR A:161 , ILE A:182 , PHE A:186 , TYR A:276 , GLY A:308 , ASP A:309 , GLN A:315 , LEU A:316 , ALA A:317 , HOH A:601 , HOH A:603 , HOH A:623 , HOH A:652 , HOH A:659 , HIS D:443 , PRO D:444BINDING SITE FOR RESIDUE FAD A 501
2AC2SOFTWAREPRO A:13 , TYR A:16 , ARG A:93 , GLY A:96 , PHE A:99 , GLU A:321 , ALA D:381 , ALA D:383 , HIS D:443 , GLU D:448 , ASN D:463 , PHE D:464BINDING SITE FOR RESIDUE M52 A 502
3AC3SOFTWARELEU B:9 , GLY B:10 , GLY B:12 , PRO B:13 , GLY B:14 , VAL B:32 , GLU B:33 , PRO B:34 , TYR B:36 , GLY B:39 , VAL B:40 , CYS B:41 , GLY B:45 , CYS B:46 , SER B:49 , LYS B:50 , TYR B:112 , GLY B:113 , ALA B:141 , THR B:142 , GLY B:143 , TYR B:161 , ILE B:182 , TYR B:276 , GLY B:308 , ASP B:309 , GLN B:315 , LEU B:316 , ALA B:317 , HIS B:318 , HOH B:601 , HOH B:607 , HOH B:620 , HIS C:443 , PRO C:444BINDING SITE FOR RESIDUE FAD B 501
4AC4SOFTWAREPRO B:13 , TYR B:16 , ARG B:93 , GLY B:96 , PHE B:99 , GLU B:321 , ALA C:381 , ALA C:383 , HIS C:443 , GLU C:448 , ASN C:463BINDING SITE FOR RESIDUE M52 B 502
5AC5SOFTWAREHIS B:443 , PRO B:444 , LEU C:9 , GLY C:10 , GLY C:12 , PRO C:13 , GLY C:14 , VAL C:32 , GLU C:33 , PRO C:34 , TYR C:36 , VAL C:40 , CYS C:41 , GLY C:45 , CYS C:46 , LYS C:50 , TYR C:112 , GLY C:113 , ALA C:141 , THR C:142 , GLY C:143 , TYR C:161 , ILE C:182 , PHE C:269 , TYR C:276 , GLY C:308 , ASP C:309 , GLN C:315 , LEU C:316 , ALA C:317 , HIS C:318 , HOH C:601 , HOH C:617 , HOH C:712BINDING SITE FOR RESIDUE FAD C 501
6AC6SOFTWAREALA B:381 , ALA B:383 , HIS B:443 , GLU B:448 , ASN B:463 , HOH B:602 , PRO C:13 , TYR C:16 , LEU C:42 , ARG C:93 , GLY C:96 , PHE C:99 , GLU C:321BINDING SITE FOR RESIDUE M52 C 502
7AC7SOFTWAREHIS A:443 , PRO A:444 , LEU D:9 , GLY D:10 , GLY D:12 , PRO D:13 , GLY D:14 , VAL D:32 , GLU D:33 , PRO D:34 , LYS D:35 , TYR D:36 , GLY D:39 , VAL D:40 , CYS D:41 , GLY D:45 , CYS D:46 , LYS D:50 , TYR D:112 , GLY D:113 , ALA D:141 , THR D:142 , GLY D:143 , TYR D:161 , ILE D:182 , TYR D:276 , GLY D:308 , ASP D:309 , GLN D:315 , LEU D:316 , ALA D:317 , HIS D:318 , HOH D:602 , HOH D:621 , HOH D:643 , HOH D:647 , HOH D:651BINDING SITE FOR RESIDUE FAD D 501
8AC8SOFTWAREALA A:381 , ALA A:383 , HIS A:443 , GLU A:448 , ASN A:463 , PRO D:13 , TYR D:16 , ARG D:93 , GLU D:321BINDING SITE FOR RESIDUE M52 D 502

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:41 -A:46
2B:41 -B:46
3C:41 -C:46
4D:41 -D:46

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Gln A:352 -Pro A:353
2His A:443 -Pro A:444
3Gln B:352 -Pro B:353
4His B:443 -Pro B:444
5Gln C:352 -Pro C:353
6His C:443 -Pro C:444
7Asp D:252 -Gly D:253
8Gln D:352 -Pro D:353
9His D:443 -Pro D:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M52)

(-) Exons   (0, 0)

(no "Exon" information available for 4M52)

(-) Sequences/Alignments

Asymmetric 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.eeeee....eeeeee....eeeeeeeeeee...eee...........eehhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee...eeeeeee....eeeeeee..eeeeeee.eeee...eee.....hhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhhh.......hhhhh.eee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhhh....eeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m52 A   0 SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     


Chain B from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.eeeeeee..eeeeee....eeeeeeeeeee...eee...........eehhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee...eeeeeee....eeeeeee..eeeeeee.eeee...eee.....hhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhhh.......hhhhh.eee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhhh....eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m52 B   0 SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     


Chain C from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeee....eeeeeeeeeee...eee...........eehhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee..eeeeeeee....eeeeeee..eeeeeee.eeee...eee.....hhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhhh.......hhhhh.eee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhhh....eeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m52 C   0 SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     


Chain D from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.eeeee....eeeeee....eeeeeeeeeee...eee...........eehhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee...eeeeeee....eeeeeee..eeeeeee.eeee...eee.....hhhhh......................eee.hhhhh...hhhhhhhhhhhhhhhhh........hhhhh.eee....eeeeee.hhhhhhhh...eeeeeee...hhhhhhhh....eeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m52 D   0 SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVTKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
   Legend:   → Mismatch (orange background)
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  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 4M52)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M52)

(-) Gene Ontology  (22, 34)

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  4m52
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  DLDH_MYCTU | P9WHH9
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  1.8.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        DLDH_MYCTO | P9WHH8: 2a8x 3ii4
        DLDH_MYCTU | P9WHH9: 2a8x 3ii4

(-) Related Entries Specified in the PDB File

2a8x 3ii4