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 :  STRUCTURE OF AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE
 
Authors :  G. Bunkoczi, X. Wu, E. Dubinina, C. Johansson, C. Smee, A. Turnbull, U. O F. Von Delft, C. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt
Date :  29 Jul 05  (Deposition) - 05 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Fatty Acid Biosynthesis, Phosphopantetheine Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Bunkoczi, S. Pasta, A. Joshi, X. Wu, K. L. Kavanagh, S. Smith, U. Oppermann
Mechanism And Substrate Recognition Of Human Holo Acp Synthase.
Chem. Biol. V. 14 1243 2007
PubMed-ID: 18022563  |  Reference-DOI: 10.1016/J.CHEMBIOL.2007.10.013

(-) Compounds

Molecule 1 - HSPC223
    Chains: A
    EC Number: 1.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: DE3
    Expression System Plasmid: PCOEX-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE- PHOSPHOPANTETHEINYL TRANSFERASE, ALPHA-AMINOADIPIC SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1BR9Ligand/IonBROMIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , ARG A:74 , ARG A:78BINDING SITE FOR RESIDUE BR A1319
2AC2SOFTWAREARG A:65 , THR A:308BINDING SITE FOR RESIDUE BR A1320
3AC3SOFTWARETRP A:29 , LYS A:84 , PRO A:312BINDING SITE FOR RESIDUE BR A1321
4AC4SOFTWAREGLN A:276 , GLN A:278BINDING SITE FOR RESIDUE BR A1322
5AC5SOFTWAREARG A:48 , THR A:295 , PRO A:296BINDING SITE FOR RESIDUE BR A1323
6AC6SOFTWARESER A:120 , HIS A:121BINDING SITE FOR RESIDUE BR A1324
7AC7SOFTWAREASN A:118 , LYS A:195BINDING SITE FOR RESIDUE BR A1325
8AC8SOFTWAREASN A:283 , PHE A:284BINDING SITE FOR RESIDUE BR A1326
9AC9SOFTWAREPRO A:102 , ASN A:118 , ILE A:119BINDING SITE FOR RESIDUE BR A1327

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BYD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BYD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BYD)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000002786183aENSE00001290916chr11:105948216-105948620405ADPPT_HUMAN1-61611A:18-71 (gaps)61
1.4ENST000002786184ENSE00000989988chr11:105950194-105950419226ADPPT_HUMAN62-137761A:72-14776
1.5ENST000002786185ENSE00001251591chr11:105961284-105961405122ADPPT_HUMAN137-177411A:147-18741
1.6bENST000002786186bENSE00000989990chr11:105962043-105962204162ADPPT_HUMAN178-231541A:188-24154
1.6dENST000002786186dENSE00002142662chr11:105965310-10596538172ADPPT_HUMAN232-255241A:242-25716
1.7cENST000002786187cENSE00002154468chr11:105967470-1059694371968ADPPT_HUMAN256-309541A:276-31843

(-) 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:283
 aligned with ADPPT_HUMAN | Q9NRN7 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
          ADPPT_HUMAN     1 MVFPAKRFCLVPSMEGVRWAFSCGTWLPSRAEWLLAVRSIQPEEKERIGQFVFARDAKAAMAGRLMIRKLVAEKLNIPWNHIRLQRTAKGKPVLAKDSSNPYPNFNFNISHQGDYAVLAAEPELQVGIDIMKTSFPGRGSIPEFFHIMKRKFTNKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDLSPLNLDIGQVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRKPDGSRHQDVPSQDDSKPTQRQFTILNFNDLMSSAVPMTPEDPSFWDCFCFTEEIPIRNGTK 308
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------....eeeee.hhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eee.....eee...........eeeeeee..eeeeeee...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..........ee...eeee..ee...eeeeeee....eeeeeeee.------------------....eeehhhhhh.........hhhhh....hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:18-71 (gaps) UniProt: 1-61                 Exon 1.4  PDB: A:72-147 UniProt: 62-137                                     ----------------------------------------Exon 1.6b  PDB: A:188-241 UniProt: 178-231            Exon 1.6d  PDB: A:242-25Exon 1.7c  PDB: A:276-318 UniProt: 256-309            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:147-187 UniProt: 137-177----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2byd A  18 LYFQG-------HMEGVRWAFSCGTWLPSRAEWLLAVRSIQPEEKERIGQFVFARDAKAAMAGRLMIRKLVAEKLNIPWNHIRLQRTAKGKPVLAKDSSNPYPNFNFNISHQGDYAVLAAEPELQVGIDIMKTSFPGRGSIPEFFHIMKRKFTNKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDLSPLNLDIGQVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRK------------------QRQFTILNFNDLMSSAVPMTPEDPSFWDCFCFTEEIPIRNGTK 318
                                |    -  |     30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      |  -         -     | 280       290       300       310        
                               22      23                                                                                                                                                                                                                                       257                276
   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 2BYD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BYD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BYD)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADPPT_HUMAN | Q9NRN7)
molecular function
    GO:0008897    holo-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0019878    lysine biosynthetic process via aminoadipic acid    The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.
    GO:0015939    pantothenate metabolic process    The chemical reactions and pathways involving pantothenate, the anion of pantothenic acid, the amide of beta-alanine and pantoic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

 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
    BR  [ 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 ]
 
  Cis Peptide Bonds
    Ser A:213 - Pro A:214   [ 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
  2byd
    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
  ADPPT_HUMAN | Q9NRN7
    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)
  1.2.1.31
    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
  ADPPT_HUMAN | Q9NRN7
    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
        ADPPT_HUMAN | Q9NRN7: 2c43 2cg5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BYD)