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(-) Description

Title :  SUBSTRATE-LIKE BINDING MODE OF INHIBITOR PT155 TO THE MYCOBACTERIUM TUBERCULOSIS ENOYL-ACP REDUCTASE INHA
 
Authors :  H. J. Li, P. Pan, C. T. Lai, N. Liu, M. Garcia-Diaz, C. Simmerling, P. J. To
Date :  05 Feb 14  (Deposition) - 30 Apr 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Bacterial Fatty Acid Biosynthesis, Conformational Profile Of Enzyme- Inhibitor Complex, Inhibition Kinetics, Substrate-Binding Loop Refolding, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Li, C. T. Lai, P. Pan, W. Yu, N. Liu, G. R. Bommineni, M. Garcia-Diaz C. Simmerling, P. J. Tonge
A Structural And Energetic Model For The Slow-Onset Inhibition Of The Mycobacterium Tuberculosis Enoyl-Acp Reductase Inha.
Acs Chem. Biol. V. 9 986 2014
PubMed-ID: 24527857  |  Reference-DOI: 10.1021/CB400896G

(-) Compounds

Molecule 1 - ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
    Chains: A, B
    EC Number: 1.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MT1531,MTCY277.05,RV1484,INHA
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: NADH-DEPENDENT ENOYL-ACP REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
11S52Ligand/Ion5-(4-AMINO-2-METHYLPHENOXY)-2-HEXYL-4-HYDROXY-1-METHYLPYRIDINIUM
22NV8Ligand/Ion3,6,9,12,15-PENTAOXAOCTADECAN-17-AMINE
3CL2Ligand/IonCHLORIDE ION
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
11S54Ligand/Ion5-(4-AMINO-2-METHYLPHENOXY)-2-HEXYL-4-HYDROXY-1-METHYLPYRIDINIUM
22NV16Ligand/Ion3,6,9,12,15-PENTAOXAOCTADECAN-17-AMINE
3CL-1Ligand/IonCHLORIDE ION
4EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:14 , ILE A:15 , ILE A:16 , SER A:20 , ILE A:21 , PHE A:41 , LEU A:63 , ASP A:64 , VAL A:65 , SER A:94 , ILE A:95 , GLY A:96 , ILE A:122 , MET A:147 , ASP A:148 , PHE A:149 , LYS A:165 , ALA A:191 , GLY A:192 , PRO A:193 , ILE A:194 , THR A:196 , ALA A:198 , 1S5 A:302 , HOH A:405 , HOH A:420 , HOH A:422 , HOH A:426 , HOH A:432 , HOH A:457 , HOH A:459 , HOH A:462binding site for residue NAD A 301
02AC2SOFTWAREGLY A:96 , MET A:98 , MET A:103 , MET A:155 , TYR A:158 , MET A:199 , NAD A:301binding site for residue 1S5 A 302
03AC3SOFTWAREGLU A:62 , ARG A:77binding site for residue CL A 303
04AC4SOFTWARESER A:19 , HIS A:24 , ARG A:195 , LYS A:233 , ASP A:234 , ALA A:235binding site for residue 2NV A 304
05AC5SOFTWAREGLY A:221 , GLN A:224 , ARG A:225binding site for residue 2NV A 305
06AC6SOFTWARETHR A:2 , TRP A:249 , THR B:2 , TRP B:249binding site for residue 2NV A 307
07AC7SOFTWAREGLY B:14 , ILE B:15 , ILE B:16 , SER B:20 , ILE B:21 , PHE B:41 , LEU B:63 , ASP B:64 , VAL B:65 , SER B:94 , ILE B:95 , GLY B:96 , ILE B:122 , MET B:147 , ASP B:148 , PHE B:149 , LYS B:165 , ALA B:191 , GLY B:192 , PRO B:193 , ILE B:194 , THR B:196 , 1S5 B:302 , HOH B:420 , HOH B:422 , HOH B:427 , HOH B:432 , HOH B:441 , HOH B:443 , HOH B:455 , HOH B:460 , HOH B:476binding site for residue NAD B 301
08AC8SOFTWAREGLY B:96 , MET B:98 , MET B:103 , ALA B:157 , TYR B:158 , MET B:199 , NAD B:301 , 2NV B:305binding site for residue 1S5 B 302
09AC9SOFTWAREASP B:42 , ARG B:43 , LEU B:44 , ARG B:45 , GLU B:62 , HIS B:70binding site for residue EPE B 303
10AD1SOFTWAREGLU B:62 , ARG B:77binding site for residue CL B 304
11AD2SOFTWAREPHE B:41 , PHE B:97 , MET B:98 , 1S5 B:302 , HOH B:440binding site for residue 2NV B 305
12AD3SOFTWAREARG B:43 , LEU B:197 , GLY B:204 , ALA B:206binding site for residue 2NV B 306
13AD4SOFTWAREPHE A:109 , ASP A:110 , GLU B:68 , TYR B:125 , LYS B:132binding site for residue 2NV B 307
14AD5SOFTWARETYR A:125 , LYS A:132 , PHE B:109 , ASP B:110binding site for residue 2NV B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OXN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OXN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OXN)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhh....eeeeee.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxn A   2 TGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL 269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      218       228       238       248       258       268 
                                                                                                                                                                                                                                 201|                                                            
                                                                                                                                                                                                                                  209                                                            


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhh....eeeeee.....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........eeeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oxn B   2 TGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL 269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 4OXN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 20)

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 Related Entries

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

UniProtKB/Swiss-Prot
        INHA_MYCTO | P9WGR0: 1bvr 1eny 1enz 1p44 1p45 1zid 2aq8 2aqh 2aqi 2aqk 2b35 2b36 2b37 2h9i 2idz 2ie0 2ieb 2ied 2nsd 2ntj 2nv6 2pr2 2x22 2x23 3fne 3fnf 3fng 3fnh 3oew 3oey 3of2 4bge 4bgi 4bii 4bqp 4bqr 4cod 4d0r 4d0s 4dqu 4dre 4dti 4ohu 4oim 4oxk 4oxy 4oyr 4trj 4trm 4trn 5cpf 5mtp
        INHA_MYCTU | P9WGR1: 1bvr 1eny 1enz 1p44 1p45 1zid 2aq8 2aqh 2aqi 2aqk 2b35 2b36 2b37 2h9i 2idz 2ie0 2ieb 2ied 2nsd 2ntj 2nv6 2pr2 2x22 2x23 3fne 3fnf 3fng 3fnh 3oew 3oey 3of2 4bge 4bgi 4bii 4bqp 4bqr 4cod 4d0r 4d0s 4dqu 4dre 4dti 4ohu 4oim 4oxk 4oxy 4oyr 4qxm 4r9r 4r9s 4trj 4trm 4trn 4tro 4tzk 4tzt 4u0j 4u0k 4uvd 4uve 4uvg 4uvh 4uvi 5coq 5cp8 5cpb 5cpf 5g0s 5g0t 5g0u 5g0v 5g0w 5jfo 5mtp 5mtq 5mtr 5ugs 5ugt 5ugu

(-) Related Entries Specified in the PDB File

4oxk