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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE IN COMPLEX WITH 2-(5-METHOXY-2-(2-NITRO-4-(TRIFLUOROMETHYL)PHENYLSULFONYLCARBAMOYL)-1H-INDOL-1-YL)ACETIC ACID
 
Authors :  H. L. Silvestre, T. L. Blundell
Date :  22 Sep 13  (Deposition) - 27 Aug 14  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Alpha Beta 3-Layer(Aba) Sandwich Rossmann Fold, Pantoate-Ligase, Atp Binding, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. W. Hung, H. L. Silvestre, S. Wen, G. P. George, J. Boland, T. L. Blundell, A. Ciulli, C. Abell
Optimization Of Inhibitors Of Mycobacterium Tuberculosis Pantothenate Synthetase Based On Group Efficiency Analysis.
Chemmedchem V. 11 38 2016
PubMed-ID: 26486566  |  Reference-DOI: 10.1002/CMDC.201500414

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    Chains: A, B
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MT3707, MTCY07H7B.20, PANC, RV3602C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
12DZ4Ligand/Ion[5-METHOXY-2-({[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]SULFONYL}CARBAMOYL)-1H-INDOL-1-YL]ACETIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
3EOH3Ligand/IonETHANOL
4GOL3Ligand/IonGLYCEROL
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
12DZ4Ligand/Ion[5-METHOXY-2-({[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]SULFONYL}CARBAMOYL)-1H-INDOL-1-YL]ACETIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
3EOH3Ligand/IonETHANOL
4GOL3Ligand/IonGLYCEROL
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
12DZ3Ligand/Ion[5-METHOXY-2-({[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]SULFONYL}CARBAMOYL)-1H-INDOL-1-YL]ACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3EOH3Ligand/IonETHANOL
4GOL3Ligand/IonGLYCEROL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:218 , HIS B:222 , THR B:225BINDING SITE FOR RESIDUE EOH A 401
02AC2SOFTWAREASN A:176 , HOH A:617 , HOH A:734BINDING SITE FOR RESIDUE EOH A 402
03AC3SOFTWAREPRO A:38 , THR A:39 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , GLN A:72 , TYR A:82 , HIS A:135 , LYS A:160 , ASP A:161 , GLN A:164 , PRO A:185 , THR A:186 , VAL A:187 , MET A:195 , SER A:196 , SER A:197 , 2DZ A:405 , GOL A:408 , HOH A:574 , HOH A:652 , HOH A:718 , HOH A:720 , HOH A:731BINDING SITE FOR RESIDUE 2DZ A 403
04AC4SOFTWAREMET A:71 , LEU A:114 , THR A:117 , PRO A:133 , THR A:134 , ALA A:137 , GLY A:138 , THR A:141 , HOH A:704 , HOH A:740 , ILE B:3 , PRO B:4 , PHE B:6 , PRO B:8 , LEU B:27 , THR B:30 , ARG B:32 , GLN B:119BINDING SITE FOR RESIDUE 2DZ A 404
05AC5SOFTWAREASP A:78 , ALA A:81 , TYR A:82 , PRO A:83 , GLU A:128 , PRO A:131 , ARG A:132 , HIS A:135 , SER A:197 , ARG A:198 , TYR A:201 , ARG A:278 , 2DZ A:403 , HOH A:515 , HOH A:614BINDING SITE FOR RESIDUE 2DZ A 405
06AC6SOFTWAREMET A:109 , TYR A:110 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , HOH A:738 , ASP B:174BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWARELEU A:114 , ARG A:115 , THR A:117 , GLN B:119 , PRO B:120 , GLY B:121BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWAREPRO A:38 , MET A:40 , GLN A:72 , VAL A:143 , GLN A:164 , 2DZ A:403 , HOH A:585 , HOH A:716BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREPRO A:111 , ASP A:112BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWAREALA A:205 , GLN A:206 , ALA A:209 , PRO A:243 , GLY A:244 , HOH A:619 , HOH A:748BINDING SITE FOR RESIDUE EOH A 410
11BC2SOFTWARELEU A:147 , GLN A:148 , ARG A:151 , ASP A:178 , VAL A:179 , HOH A:537 , HOH A:709 , GLN B:148 , ARG B:151BINDING SITE FOR RESIDUE EDO A 411
12BC3SOFTWAREALA A:21 , SER A:24 , ARG A:25 , GLN A:148 , ILE A:149 , VAL A:150 , ARG A:151 , ASP B:178BINDING SITE FOR RESIDUE GOL A 412
13BC4SOFTWAREPRO B:38 , THR B:39 , MET B:40 , HIS B:44 , GLY B:46 , HIS B:47 , HIS B:135 , VAL B:139 , VAL B:143 , PHE B:157 , LYS B:160 , ASP B:161 , GLN B:164 , PRO B:185 , THR B:186 , VAL B:187 , MET B:195 , SER B:196 , SER B:197 , HOH B:541 , HOH B:551 , HOH B:713 , HOH B:717 , HOH B:722 , HOH B:728BINDING SITE FOR RESIDUE 2DZ B 401
14BC5SOFTWAREASP A:174 , MET B:109 , TYR B:110 , GLY B:113 , ARG B:115 , THR B:116 , LYS B:145 , HOH B:537BINDING SITE FOR RESIDUE EDO B 402
15BC6SOFTWAREGLN A:148 , ARG A:151 , LEU B:147 , GLN B:148 , ASP B:178 , VAL B:179 , HOH B:506 , HOH B:544BINDING SITE FOR RESIDUE EDO B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUN)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhh.hhhhh..hhhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mun A   4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    13        23        33        43        53        63        73|       86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286   
                                                                                                73|                                                                                                                                                                                                                    
                                                                                                 77                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mun B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEI 287
                                    11        21        31        41        51        61        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
                                                                                               70|                                                                                                                                                                                                          
                                                                                                85
   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 4MUN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 20)

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  6.3.2.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_MYCTO | P9WIL4: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul
        PANC_MYCTU | P9WIL5: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a7x 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul

(-) Related Entries Specified in the PDB File

4mq6 4mue 4muf 4mug 4muh 4mui 4muk 4mul