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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE YJEE PROTEIN
 
Authors :  A. Teplyakov, G. L. Gilliland, Structure 2 Function Project (S2F)
Date :  13 Aug 00  (Deposition) - 07 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Nucleotide-Binding Fold, Structural Genomics, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Teplyakov, G. Obmolova, M. Tordova, N. Thanki, N. Bonander, E. Eisenstein, A. J. Howard, G. L. Gilliland
Crystal Structure Of The Yjee Protein From Haemophilus Influenzae: A Putative Atpase Involved In Cell Wall Synthesis
Proteins V. 48 220 2002
PubMed-ID: 12112691  |  Reference-DOI: 10.1002/PROT.10114
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN HI0065
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLASMID T7-HIS TAG
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1HG3Ligand/IonMERCURY (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:103 , PHE A:104 , CYS A:110BINDING SITE FOR RESIDUE HG A 200
2AC2SOFTWAREMET B:35 , PHE B:84 , PHE B:104 , CYS B:110BINDING SITE FOR RESIDUE HG B 200
3AC3SOFTWAREMET C:35 , TYR C:103 , PHE C:104 , CYS C:110BINDING SITE FOR RESIDUE HG C 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FL9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FL9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FL9)

(-) Exons   (0, 0)

(no "Exon" information available for 1FL9)

(-) 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:157
 aligned with TSAE_HAEIN | P44492 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           TSAE_HAEIN     1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
               SCOP domains d1fl9a_ A: Hypothetical protein HI0065                                                                                                                        SCOP domains
               CATH domains 1fl9A00 A:1-157 P-loop containing nucleotide triphosphate hydrolases                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..............eeeee....eeeeee.....hhhhhhhhhhhh.....eeeeee.............eeeeeee....eeeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl9 A   1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with TSAE_HAEIN | P44492 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           TSAE_HAEIN     1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
               SCOP domains d1fl9b_ B: Hypothetical protein HI0065                                                                                                                        SCOP domains
               CATH domains 1fl9B00 B:1-157 P-loop containing nucleotide triphosphate hydrolases                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhh............eee.......eeeee......hhhhhhh..........eeeee.hhhhh.......eeeeeee....eeeeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl9 B   1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with TSAE_HAEIN | P44492 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           TSAE_HAEIN     1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
               SCOP domains d1fl9c_ C: Hypothetical protein HI0065                                                                                                                        SCOP domains
               CATH domains 1fl9C00 C:1-157 P-loop containing nucleotide triphosphate hydrolases                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhhhhhhhhhhhh.......eee......hhhhhhhhhhhhhh.............eeeee..eeeeeee.....hhhhhhhhh..........eeee..................ee....ee........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl9 C   1 MESLTQYIPDEFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEWSEKGQGILPEADILVNIDYYDDARNIELIAQTNLGKNIISAFS 157
                                    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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FL9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (TSAE_HAEIN | P44492)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002949    tRNA threonylcarbamoyladenosine modification    The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
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
    HG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fl9)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  1fl9
    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
  TSAE_HAEIN | P44492
    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
  TSAE_HAEIN | P44492
    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
        TSAE_HAEIN | P44492: 1htw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FL9)