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

(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE/PPAT FROM PSEUDOMONAS AERUGINOSA WITH COA
 
Authors :  R. Chatterjee, S. Datta
Date :  24 Nov 14  (Deposition) - 25 Nov 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rossmann Fold Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chatterjee, A. Mondal, A. Basu, S. Datta
Transition Of Phosphopantetheine Adenylyltransferase From Catalytic To Allosteric State Is Characterized By Ternary Complex Formation In Pseudomonas Aeruginosa
Biochim. Biophys. Acta V. 1864 773 2016
PubMed-ID: 27041211  |  Reference-DOI: 10.1016/J.BBAPAP.2016.03.018

(-) Compounds

Molecule 1 - PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.7.7.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: COAD, PA0363, PA2G_04277
    Organism Scientific: PSEUDOMONAS AERUGINOSA 2192
    Organism Taxid: 350703
    Synonym: DEPHOSPHO-COA PYROPHOSPHORYLASE, PANTETHEINE-PHOSPHATE ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2COA3Ligand/IonCOENZYME A
3DMS7Ligand/IonDIMETHYL SULFOXIDE
4FMT1Ligand/IonFORMIC ACID
5PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:8 , THR A:9 , ALA A:36 , LYS A:41 , THR A:71 , LEU A:72 , LEU A:73 , ARG A:87 , TYR A:97 , LEU A:101 , SER A:127 , SER A:128 , THR A:129 , ARG A:132 , HOH A:311 , HOH A:320 , LEU C:130 , GLU C:133 , LEU C:137BINDING SITE FOR RESIDUE COA A 201
02AC2SOFTWARELYS A:15 , GLY A:18 , ASP A:19BINDING SITE FOR RESIDUE DMS A 202
03AC3SOFTWAREGLY A:68 , PHE A:69 , SER A:70 , THR A:71 , PHE A:76 , PEG A:209BINDING SITE FOR RESIDUE DMS A 203
04AC4SOFTWAREALA A:135 , GLY A:138 , GLY A:139 , ASP A:140 , ILE A:141 , ALA A:154 , LYS B:81BINDING SITE FOR RESIDUE DMS A 204
05AC5SOFTWAREGLU A:155 , ARG A:156 , LYS A:158 , GLN C:55 , VAL C:66BINDING SITE FOR RESIDUE DMS A 205
06AC6SOFTWAREGLU A:48 , GLN A:49 , LEU C:47 , GLY C:68BINDING SITE FOR RESIDUE ACT A 206
07AC7SOFTWARESER A:70 , PEG A:209 , HIS C:75BINDING SITE FOR RESIDUE ACT A 207
08AC8SOFTWAREGLY A:16 , HIS A:17 , GLY A:88 , ARG A:90BINDING SITE FOR RESIDUE ACT A 208
09AC9SOFTWARELEU A:47 , SER A:70 , DMS A:203 , ACT A:207BINDING SITE FOR RESIDUE PEG A 209
10BC1SOFTWAREGLU A:48 , VAL A:67 , GLY A:68 , FMT A:212 , THR C:71BINDING SITE FOR RESIDUE PEG A 210
11BC2SOFTWAREALA A:52 , ALA A:148BINDING SITE FOR RESIDUE PEG A 211
12BC3SOFTWAREGLU A:48 , VAL A:51 , ALA A:52 , GLN A:55 , PEG A:210BINDING SITE FOR RESIDUE FMT A 212
13BC4SOFTWARELEU A:137 , PRO B:7 , GLY B:8 , THR B:9 , ALA B:36 , LYS B:41 , THR B:71 , LEU B:72 , LEU B:73 , ARG B:87 , TYR B:97 , LEU B:101 , SER B:127 , SER B:128 , THR B:129 , HOH B:302 , HOH B:303 , HOH B:307 , HOH B:324BINDING SITE FOR RESIDUE COA B 201
14BC5SOFTWAREARG B:26 , ASN B:83 , ASP B:111BINDING SITE FOR RESIDUE DMS B 202
15BC6SOFTWAREPRO A:147 , MET B:1 , ARG B:3 , LYS B:81 , ASN B:83BINDING SITE FOR RESIDUE DMS B 203
16BC7SOFTWARELYS B:15 , ASP B:19 , GLU B:22BINDING SITE FOR RESIDUE ACT B 204
17BC8SOFTWARELEU B:130 , GLY C:8 , THR C:9 , LYS C:41 , PHE C:69 , LEU C:73 , ARG C:87 , ARG C:90 , TYR C:97 , LEU C:101 , ASN C:105 , SER C:127 , SER C:128 , THR C:129 , HOH C:306 , HOH C:311BINDING SITE FOR RESIDUE COA C 201
18BC9SOFTWAREASN A:83 , ASP A:111 , GLU A:113 , ARG C:26 , LEU C:27BINDING SITE FOR RESIDUE DMS C 202
19CC1SOFTWARELYS C:15 , GLY C:18BINDING SITE FOR RESIDUE ACT C 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X1M)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp A:11 -Pro A:12
2Ala A:91 -Val A:92
3Asp B:11 -Pro B:12
4Asp C:11 -Pro C:12
5Val C:92 -Ser C:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X1M)

(-) Exons   (0, 0)

(no "Exon" information available for 3X1M)

(-) Sequences/Alignments

Asymmetric/Biological 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeeee.hhhhh...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...eeeee..hhhhh..hhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x1m A   1 MNRVLYPGTFDPITKGHGDLIERASRLFDHVIIAVAASPKKNPLFSLEQRVALAQEVTKHLPNVEVVGFSTLLAHFVKEQKANVFLRGLRAVSDFEYEFQLANMNRQLAPDVESMFLTPSEKYSFISSTLVREIAALGGDISKFVHPAVADALAERFK 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeeee.hhhhh...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhh...eeeee.......hhhhhhhhhhhhhh...eeeee..hhhhh..hhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x1m B   1 MNRVLYPGTFDPITKGHGDLIERASRLFDHVIIAVAASPKKNPLFSLEQRVALAQEVTKHLPNVEVVGFSTLLAHFVKEQKANVFLRGLRAVSDFEYEFQLANMNRQLAPDVESMFLTPSEKYSFISSTLVREIAALGGDISKFVHPAVADALAERFK 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        


Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh.eeeeeee.hhhhh...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhh...eeeee.......hhhhhhhhhhhhhh...eeeee..hhhhh..hhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x1m C   1 MNRVLYPGTFDPITKGHGDLIERASRLFDHVIIAVAASPKKNPLFSLEQRVALAQEVTKHLPNVEVVGFSTLLAHFVKEQKANVFLRGLRAVSDFEYEFQLANMNRQLAPDVESMFLTPSEKYSFISSTLVREIAALGGDISKFVHPAVADALAERFK 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 3X1M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X1M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X1M)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3X1M)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    COA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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:91 - Val A:92   [ RasMol ]  
    Asp A:11 - Pro A:12   [ RasMol ]  
    Asp B:11 - Pro B:12   [ RasMol ]  
    Asp C:11 - Pro C:12   [ RasMol ]  
    Val C:92 - Ser C:93   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3x1m
    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
  A0A0X1KGP2_P | A0A0X1KGP2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.3
    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
  A0A0X1KGP2_P | A0A0X1KGP2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0X1KGP2_P | A0A0X1KGP2: 3x1j 3x1k 4ruk

(-) Related Entries Specified in the PDB File

3x1j 3x1k 4ruk