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 THE LP_1622 PROTEIN FROM LACTOBACILLUS PLANTARUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LPR114
 
Authors :  S. M. Vorobiev, M. Abashidze, J. Seetharaman, L. Zhao, M. Maglaqui, E. L. Foote, C. Ciccosanti, H. Janjua, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  02 Apr 08  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Q88Wk7_lacpl, Transferase, Thiamine Pyrophosphokinase, Nesg, Lpr114, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, M. Abashidze, J. Seetharaman, L. Zhao, M. Maglaqui, E. L. Foote, C. Ciccosanti, H. Janjua, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Lp_1622 Protein From Lactobacillus Plantarum.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN LP_1622
    Atcc: BAA-793
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21-23C
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LP_1622
    Organism Scientific: LACTOBACILLUS PLANTARUM WCFS1
    Organism Taxid: 220668
    Strain: WCFS1 / NCIMB 8826

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1MSE17Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:139 , ILE C:148 , THR C:149BINDING SITE FOR RESIDUE SO4 C 301
2AC2SOFTWARETHR C:13 , ARG C:36 , LYS C:39 , ARG C:40BINDING SITE FOR RESIDUE SO4 C 302
3AC3SOFTWARETHR B:13 , ARG B:32 , ARG B:36 , LYS B:39 , ARG B:40BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWAREARG A:139 , ILE A:148 , THR A:149BINDING SITE FOR RESIDUE SO4 A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CQ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CQ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3CQ9)

(-) 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:202
 aligned with F9UNZ6_LACPL | F9UNZ6 from UniProtKB/TrEMBL  Length:219

    Alignment length:211
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 
         F9UNZ6_LACPL     3 TIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVMVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANMWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLMPMHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRD 213
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh..hhhhh...eeeehhhhhhhhhh.....eee...---------hhhhhhhh.eee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeee...eeeeee..eeeeee......eeeeee...eeeee......eeeeee.....eeee.....eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cq9 A   3 TIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVmVVGDF---------TVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANmWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLmPmHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRD 213
                                    12        22        32        42   |    |-        62        72        82        92       102       112 |     122       132       142       152       162| |    172       182       192       202       212 
                                                                      46-MSE1        61                                                  114-MSE                                          163-MSE                                              
                                                                                                                                                                                            165-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with F9UNZ6_LACPL | F9UNZ6 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                                                                                                                                                                                                                                  219  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      |  
         F9UNZ6_LACPL     3 TIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVMVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANMWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLMPMHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDDSMADA--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh..hhhhh...eeeehhhhhhhhhh.....eee......hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeee...eeeeee..eeeeee......eeeeee...eeeee......eeeeee.....eeee.....eeeeee....eeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cq9 B   3 TIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVmVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANmWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLmPmHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDDSmADALE 221
                                    12        22        32        42   |    52        62        72        82        92       102       112 |     122       132       142       152       162| |    172       182       192       202       212   |     
                                                                      46-MSE                                                             114-MSE                                          163-MSE                                              216-MSE 
                                                                                                                                                                                            165-MSE                                                    


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with F9UNZ6_LACPL | F9UNZ6 from UniProtKB/TrEMBL  Length:219

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         F9UNZ6_LACPL     2 ATIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVMVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANMWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLMPMHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDD 214
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhh..hhhhh...eeeehhhhhhhhhh.....eee......hhhhhhhhhhhh...eee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh.hhhhhhh.eeeee..eeeeee..eeeeee......eeeeee...eeeee......eeeeee.....eeee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cq9 C   2 ATIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVmVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANmWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLmPmHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDD 214
                                    11        21        31        41    |   51        61        71        81        91       101       111  |    121       131       141       151       161 | |   171       181       191       201       211   
                                                                       46-MSE                                                             114-MSE                                          163-MSE                                               
                                                                                                                                                                                             165-MSE                                             


Chain D from PDB  Type:PROTEIN  Length:203
 aligned with F9UNZ6_LACPL | F9UNZ6 from UniProtKB/TrEMBL  Length:219

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         F9UNZ6_LACPL     2 ATIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVMVVGDFDSIDAAELQTVKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANMWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLMPMHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDD 214
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhh..hhhhh...eeeehhhhhhhhhh.....eee...----------........eee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeee...eeeeee..eeeeee......eeeeee...eeeee......eeeeee.....eeee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cq9 D   2 ATIVNLLVGGPTANYPADLTTIPGPWVGADRGALRLVKRGIQPVmVVGDF----------VKDALVGAIVVKPDQDHTDTQLAIKSIFEQLQPDEVHLYGATGGRLDHLLANmWLVLDPVFRQWAPQIKLIDKQNSVRFFLPGDYQITKEADKRYLAFVPLmPmHLTLPDEKYQLDAAYNAYPISWASNEFSGNTGHFSFDAGVLAVIQSRDD 214
                                    11        21        31        41    |   51         -|       71        81        91       101       111  |    121       131       141       151       161 | |   171       181       191       201       211   
                                                                       46-MSE1         62                                                 114-MSE                                          163-MSE                                               
                                                                                                                                                                                             165-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  (0, 0)

(no "SCOP Domain" information available for 3CQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CQ9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (F9UNZ6_LACPL | F9UNZ6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0030975    thiamine binding    Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0004788    thiamine diphosphokinase activity    Catalysis of the reaction: ATP + thiamine = AMP + thiamine diphosphate.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
    GO:0006772    thiamine metabolic process    The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

 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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cq9)
 
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
  3cq9
    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
  F9UNZ6_LACPL | F9UNZ6
    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)
  (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
  F9UNZ6_LACPL | F9UNZ6
    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 3CQ9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CQ9)