Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE IN COMPLEX WITH 2-(2-(BENZYLSULFONYLCARBAMOYL)-5-METHOXY-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 :  1.92
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, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
12DU3Ligand/Ion{2-[(BENZYLSULFONYL)CARBAMOYL]-5-METHOXY-1H-INDOL-1-YL}ACETIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EOH6Ligand/IonETHANOL
4GOL1Ligand/IonGLYCEROL
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
12DU3Ligand/Ion{2-[(BENZYLSULFONYL)CARBAMOYL]-5-METHOXY-1H-INDOL-1-YL}ACETIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EOH6Ligand/IonETHANOL
4GOL1Ligand/IonGLYCEROL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
12DU2Ligand/Ion{2-[(BENZYLSULFONYL)CARBAMOYL]-5-METHOXY-1H-INDOL-1-YL}ACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3EOH1Ligand/IonETHANOL
4GOL1Ligand/IonGLYCEROL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:115 , THR A:117 , GLN B:119 , PRO B:120 , 2DU B:402BINDING SITE FOR RESIDUE EOH A 401
02AC2SOFTWARETHR A:218 , HIS B:222 , THR B:225BINDING SITE FOR RESIDUE EOH A 402
03AC3SOFTWAREASN A:176 , HOH A:690BINDING SITE FOR RESIDUE EOH A 403
04AC4SOFTWAREPRO A:38 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , VAL A:143 , PHE A:157 , GLN A:164 , PRO A:185 , VAL A:187 , MET A:195 , SER A:196 , SER A:197 , HOH A:570BINDING SITE FOR RESIDUE 2DU A 404
05AC5SOFTWAREMET A:109 , TYR A:110 , GLY A:113 , LEU A:114 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREARG A:154BINDING SITE FOR RESIDUE EOH A 406
07AC7SOFTWAREGLY A:74 , ARG A:132 , PRO A:133 , THR A:134 , HIS A:135 , HOH A:681BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREMET A:71 , TYR A:110BINDING SITE FOR RESIDUE EOH A 408
09AC9SOFTWAREPRO B:38 , THR B:39 , MET B:40 , HIS B:44 , GLY B:46 , HIS B:47 , GLY B:158 , LYS B:160 , VAL B:184 , PRO B:185 , THR B:186 , VAL B:187 , MET B:195 , HOH B:540 , HOH B:542 , HOH B:637 , HOH B:670BINDING SITE FOR RESIDUE 2DU B 401
10BC1SOFTWAREMET A:71 , LEU A:114 , PRO A:133 , THR A:134 , EOH A:401 , ILE B:3 , PRO B:4 , PHE B:6 , PRO B:8 , LEU B:27 , THR B:30 , ARG B:32 , GLN B:119 , HOH B:503BINDING SITE FOR RESIDUE 2DU B 402
11BC2SOFTWARETYR B:110 , LEU B:114 , GLY B:138 , THR B:141BINDING SITE FOR RESIDUE GOL B 403
12BC3SOFTWAREGLY B:244 , ARG B:273 , GLY B:275BINDING SITE FOR RESIDUE EDO B 404
13BC4SOFTWAREPHE B:67 , PRO B:104 , TYR B:110 , HOH B:674BINDING SITE FOR RESIDUE EDO B 405
14BC5SOFTWAREASP A:174 , TYR B:110 , GLY B:113 , ARG B:115 , THR B:116 , LYS B:145BINDING SITE FOR RESIDUE EDO B 406
15BC6SOFTWAREGLN A:148 , ARG A:151 , GLN B:148 , ASP B:178 , HOH B:533BINDING SITE FOR RESIDUE EOH B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:74 -Ala A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUJ)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeeeeeeee..........eeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4muj A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTF 290
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282        


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..eeeeeeee...hhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4muj B   1 MAIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    10        20        30        40        50        60       |86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
                                                                                              68|                                                                                                                                                                                                           
                                                                                               85
   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 4MUJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 20)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    2DU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EOH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:74 - Ala A:75   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4muj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PANC_MYCTO | P9WIL4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PANC_MYCTU | P9WIL5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PANC_MYCTO | P9WIL4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PANC_MYCTU | P9WIL5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4muk 4mul 4mun
        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 4muk 4mul 4mun

(-) Related Entries Specified in the PDB File

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