Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Biol. Unit 4:  A  (2x)
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN PLSX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PLSX, BSU15890
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x):  B
Biological Unit 4 (2x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VI1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:13 -Pro A:14
2Ala B:13 -Pro B:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI1)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI1)

(-) 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:327
 aligned with PLSX_BACSU | P71018 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:334
                             1                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
           PLSX_BACSU     - -MRIAVDAMGGDHAPKAVIDGVIKGIEAFDDLHITLVGDKTTIESHLTTTSDRITVLHADEVIEPTDEPVRAVRRKKNSSMVLMAQEVAENRADACISAGNTGALMTAGLFIVGRIKGIDRPALAPTLPTVSGDGFLLLDVGANVDAKPEHLVQYAIMGSVYSQQVRGVTSPRVGLLNVGTEDKKGNELTKQTFQILKETANINFIGNVEARDLLDDVADVVVTDGFTGNVTLKTLEGSALSIFKMMRDVMTSTLTSKLAAAVLKPKLKEMKMKMEYSNYGGASLFGLKAPVIKAHGSSDSNAVFHAIRQAREMVSQNVAALIQEEVKEEKTDE 333
               SCOP domains d1vi1a_ A: Fatty acid/phospholipid synthesis protein PlsX                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1vi1A00 A:0-333 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeeeehhhhhhh........eeeee.........hhhhhhhhh..hhhhhhhhhhhh....eeee..hhhhhhhhhhhh..........eee.ee.......eeee........hhhhhhhhhhhhhhhhhhh......eeeeee........hhhhhhhhhhhhh....eeeeeee.hhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------.hhhhhhhhhhhhhhhhh..eeee.....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi1 A   0 SLRIAVDAmGGDHAPKAVIDGVIKGIEAFDDLHITLVGDKTTIESHLTTTSDRITVLHADEVIEPTDEPVRAVRRKKNSSmVLmAQEVAENRADACISAGNTGALmTAGLFIVGRIKGIDRPALAPTLPTVSGDGFLLLDVGANVDAKPEHLVQYAImGSVYSQQVRGVTSPRVGLLNVGTEDKKGNELTKQTFQILKETANINFIGNVEARDLLDDVADVVVTDGFTGNVTLKTLEGSALSIFKmmRDVmTSTL-------VLKPKLKEmKmKmEYSNYGGASLFGLKAPVIKAHGSSDSNAVFRAIRQAREmVSQNVAALIQEEVKEEKTDE 333
                                    |9        19        29        39        49        59        69        79|  |    89        99     | 109       119       129       139       149       159       169       179       189       199       209       219       229       239     ||249|   |    -  |    269| | |  279       289       299       309   |   319       329    
                                    8-MSE                                                                  80-MSE                  105-MSE                                             157-MSE                                                                                 245-MSE| 254     262     270-MSE                                    313-MSE                
                                                                                                              83-MSE                                                                                                                                                            246-MSE                   272-MSE                                                         
                                                                                                                                                                                                                                                                                    250-MSE                 274-MSE                                                       


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with PLSX_BACSU | P71018 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:329
                             1                                                                                                                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
           PLSX_BACSU     - -MRIAVDAMGGDHAPKAVIDGVIKGIEAFDDLHITLVGDKTTIESHLTTTSDRITVLHADEVIEPTDEPVRAVRRKKNSSMVLMAQEVAENRADACISAGNTGALMTAGLFIVGRIKGIDRPALAPTLPTVSGDGFLLLDVGANVDAKPEHLVQYAIMGSVYSQQVRGVTSPRVGLLNVGTEDKKGNELTKQTFQILKETANINFIGNVEARDLLDDVADVVVTDGFTGNVTLKTLEGSALSIFKMMRDVMTSTLTSKLAAAVLKPKLKEMKMKMEYSNYGGASLFGLKAPVIKAHGSSDSNAVFHAIRQAREMVSQNVAALIQEEVKE 328
               SCOP domains d1vi1b_ B: Fatty acid/phospholipid synthesis protein PlsX                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1vi1B00 B:0-328 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) --FA_synthesis-1vi1B01 B:2-321                                                                                                                                                                                                                                                                                                    ------- Pfam domains (1)
           Pfam domains (2) --FA_synthesis-1vi1B02 B:2-321                                                                                                                                                                                                                                                                                                    ------- Pfam domains (2)
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeeeehhhhhhh........eeeee.........hhhhhhhhh..hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.........eee.ee.......eeee........hhhhhhhhhhhhhhhhhhh......eeeeee........hhhhhhhhhhhhh....eeeeeee.hhh......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....--------.hhhhhhhhhhhhhhh.eeee.....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi1 B   0 SLRIAVDAmGGDHAPKAVIDGVIKGIEAFDDLHITLVGDKTTIESHLTTTSDRITVLHADEVIEPTDEPVRAVRRKKNSSmVLmAQEVAENRADACISAGNTGALmTAGLFIVGRIKGIDRPALAPTLPTVSGDGFLLLDVGANVDAKPEHLVQYAImGSVYSQQVRGVTSPRVGLLNVGTEDKKGNELTKQTFQILKETANINFIGNVEARDLLDDVADVVVTDGFTGNVTLKTLEGSALSIFKmmRDVmTSTLTS--------PKLKEmKmKmEYSNYGGASLFGLKAPVIKAHGSSDSNAVFRAIRQAREmVSQNVAALIQEEVKE 328
                                    |9        19        29        39        49        59        69        79|  |    89        99     | 109       119       129       139       149       159       169       179       189       199       209       219       229       239     ||249|     |  -     | 269| | |  279       289       299       309   |   319         
                                    8-MSE                                                                  80-MSE                  105-MSE                                             157-MSE                                                                                 245-MSE|   256      265    | | |                                    313-MSE           
                                                                                                              83-MSE                                                                                                                                                            246-MSE                 270-MSE                                                      
                                                                                                                                                                                                                                                                                    250-MSE               272-MSE                                                    
                                                                                                                                                                                                                                                                                                            274-MSE
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PLSX_BACSU | P71018)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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.
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0006644    phospholipid metabolic process    The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1vi1)
 
  Cis Peptide Bonds
    Ala A:13 - Pro A:14   [ RasMol ]  
    Ala B:13 - Pro B:14   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  1vi1
    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
  PLSX_BACSU | P71018
    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)
  (no 'Enzyme Classificator' available)
    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
  PLSX_BACSU | P71018
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1VI1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VI1)