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 :  PANTOTHENATE SYNTHETASE IN COMPLEX WITH 1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID
 
Authors :  H. L. Silvestre, T. L. Blundell, C. Abell, A. Ciulli
Date :  06 Jul 12  (Deposition) - 26 Jun 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Rossmann Fold, Atp + (R)-Pantoate + Beta-Alanine, Citoplasm, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Silvestre, T. L. Blundell, C. Abell, A. Ciulli
Integrated Biophysical Approach To Fragment Screening And Validation For Fragment-Based Lead Discovery.
Proc. Natl. Acad. Sci. Usa V. 110 12984 2013
PubMed-ID: 23872845  |  Reference-DOI: 10.1073/PNAS.1304045110

(-) 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: ROSETTA 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MT3707, MTCY07H7B.20, PANC, RV3602C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    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, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
10W13Ligand/Ion1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID
2EDO7Ligand/Ion1,2-ETHANEDIOL
3EOH7Ligand/IonETHANOL
4GOL2Ligand/IonGLYCEROL
Biological Unit 1 (4, 19)
No.NameCountTypeFull Name
10W13Ligand/Ion1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID
2EDO7Ligand/Ion1,2-ETHANEDIOL
3EOH7Ligand/IonETHANOL
4GOL2Ligand/IonGLYCEROL
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
10W11Ligand/Ion1,3-DIMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
3EOH3Ligand/IonETHANOL
4GOL1Ligand/IonGLYCEROL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:748 , HOH A:758BINDING SITE FOR RESIDUE EOH A 401
02AC2SOFTWARETHR A:218 , HIS B:222 , THR B:225 , HOH B:502BINDING SITE FOR RESIDUE EOH A 402
03AC3SOFTWAREASN A:176 , GLY B:18BINDING SITE FOR RESIDUE EOH A 403
04AC4SOFTWAREMET A:109 , TYR A:110 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREARG A:188 , SER A:214 , THR A:218 , ILE A:283 , HOH A:639 , HOH A:640BINDING SITE FOR RESIDUE 0W1 A 405
06AC6SOFTWAREHIS A:44 , GLY A:46 , HIS A:47 , LYS A:160 , EDO A:409 , HOH A:630BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREPRO A:38 , GLN A:72 , VAL A:142 , HOH A:586BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREPHE B:6 , ALA B:26 , LEU B:27 , HOH B:718BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREGLY A:46 , GLY A:158 , GLU A:159 , LYS A:160 , VAL A:184 , PRO A:185 , THR A:186 , VAL A:187 , EDO A:406 , HOH A:630BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWAREGLY B:46 , HIS B:47 , LEU B:50 , PRO B:185 , THR B:186 , VAL B:187 , MET B:195 , EDO B:404 , HOH B:552 , HOH B:634 , HOH B:757 , HOH B:771BINDING SITE FOR RESIDUE 0W1 B 401
11BC2SOFTWAREARG B:188 , SER B:214 , THR B:218 , ILE B:283 , HOH B:648 , HOH B:745BINDING SITE FOR RESIDUE 0W1 B 402
12BC3SOFTWAREGLY B:244 , ARG B:273 , GLY B:275 , HOH B:510BINDING SITE FOR RESIDUE EDO B 403
13BC4SOFTWAREHIS B:44 , SER B:197 , 0W1 B:401 , HOH B:558 , HOH B:757 , HOH B:758BINDING SITE FOR RESIDUE EDO B 404
14BC5SOFTWAREASP A:174 , TYR B:110 , GLY B:113 , LEU B:114 , ARG B:115 , THR B:116 , LYS B:145BINDING SITE FOR RESIDUE EDO B 405
15BC6SOFTWAREARG B:236 , HOH B:667 , HOH B:674 , HOH B:687BINDING SITE FOR RESIDUE EOH B 406
16BC7SOFTWARESER B:15 , ALA B:16 , ALA B:108 , HOH B:606 , HOH B:720BINDING SITE FOR RESIDUE EOH B 407
17BC8SOFTWAREASP B:254 , GLY B:256BINDING SITE FOR RESIDUE EOH B 408
18BC9SOFTWAREGLN A:148 , ARG A:151 , HOH A:749 , GLN B:148 , ASP B:178 , VAL B:179 , HOH B:546BINDING SITE FOR RESIDUE EOH B 409
19CC1SOFTWAREPRO B:38 , PHE B:67 , GLN B:72 , VAL B:142 , HOH B:540 , HOH B:756BINDING SITE FOR RESIDUE GOL B 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:75 -Gly A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FZJ)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4fzja_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                         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.............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fzj A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4fzjb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.......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
                 4fzj B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    11        21        31        41        51        61        71||      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
                                                                                                 72|                                                                                                                                                                                                           
                                                                                                  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    0W1  [ 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 ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:75 - Gly A:76   [ 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
  4fzj
    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 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 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 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun

(-) Related Entries Specified in the PDB File

4ddh 4ddk 4ddm 4de5 4ef6 4efk