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

(-) Description

Title :  X-RAY STRUCTURE OF YJHP FROM E.COLI NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER13
 
Authors :  A. Kuzin, P. Manor, J. Benach, P. Smith, B. Rost, R. Xiao, G. Montelione, J. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  03 Jan 03  (Deposition) - 28 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, P. Manor, J. Benach, P. Smith, B. Rost, R. Xiao, G. Montelione, J. Hunt
X-Ray Structure Of Yjhp From E. Coli Northeast Structural Genomics Research Consortium (Nesg) Target Er13
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YJHP
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 19)

Asymmetric/Biological Unit (1, 19)
No.NameCountTypeFull Name
1MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1NKV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NKV)

(-) 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:245
 aligned with YJHP_ECOLI | P39367 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
           YJHP_ECOLI     4 PRIFTISESEHRIHNPFTEEKYATLGRVLRMKPGTRILDLGSGSGEMLCTWARDHGITGTGIDMSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGIMLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEMVLADQEGWDRYEAAKWLTMRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIAR 248
               SCOP domains d1nkva_ A: Hypothetical Protein YjhP                                                                                                                                                                                                                  SCOP domains
               CATH domains 1nkvA00 A:4-248 Vaccinia Virus protein VP39                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...........eeeeeee.hhhhh..hhhhhhhhh..eeeeeeeeeeeeee.....hhhhhhh....hhhhh.hhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nkv A   4 PRIFTISESEHRIHNPFTEEKYATLGRVLRmKPGTRILDLGSGSGEmLCTWARDHGITGTGIDmSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGImLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEmVLADQEGWDRYEAAKWLTmRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIAR 248
                                    13        23        33|       43      | 53        63   |    73        83        93       103       113       123       133  |    143       153       163       173       183|      193       203       213       223       233       243     
                                                         34-MSE          50-MSE           67-MSE                                                              136-MSE                                         184-MSE            203-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with YJHP_ECOLI | P39367 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                                                                                                                                                                                                                                                               248 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     | 
           YJHP_ECOLI     3 IPRIFTISESEHRIHNPFTEEKYATLGRVLRMKPGTRILDLGSGSGEMLCTWARDHGITGTGIDMSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGIMLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEMVLADQEGWDRYEAAKWLTMRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIAR-   -
               SCOP domains d1nkvb_ B: Hypothetical Protein YjhP                                                                                                                                                                                                                    SCOP domains
               CATH domains 1nkvB00 B:3-249 Vaccinia Virus protein VP39                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.........hhhhhhhhhhhh.......eeee....hhhhhhhhhhhh...eee..--hhhhhhhhhhhhhh.....eee------......eeeeee..--------..hhhhhhh.eeeeeeeeee..ee.....hhhhhhhh...hhhhh.hhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.ee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nkv B   3 IPRIFTISESEHRIHNPFTEEKYATLGRVLRmKPGTRILDLGSGSGEmLCTWARDHGITGTGIDm--LFTAQAKRRAEELGVSERVHFI------YVANEKCDVAACVG--------AGAEELLAQSLKPGGImLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEmVLADQEGWDRYEAAKWLTmRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIARL 249
                                    12        22        32 |      42       |52        62    |  |72        82        |-     | 102        |-       122       132   |   142       152       162       172       182 |     192       202|      212       222       232       242       
                                                          34-MSE          50-MSE           67-MSE                  91     98          111      120             136-MSE                                         184-MSE            203-MSE                                          


Chain C from PDB  Type:PROTEIN  Length:249
 aligned with YJHP_ECOLI | P39367 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:253
                                                                                                                                                                                                                                                                                 248     
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       | -   
           YJHP_ECOLI     1 MDIPRIFTISESEHRIHNPFTEEKYATLGRVLRMKPGTRILDLGSGSGEMLCTWARDHGITGTGIDMSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEKCDVAACVGATWIAGGFAGAEELLAQSLKPGGIMLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEMVLADQEGWDRYEAAKWLTMRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIAR-----   -
               SCOP domains d1nkvc_ C: Hypothetical Protein YjhP                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nkvC00 C:2-253 Vaccinia Virus protein VP39                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh..........hhhhhhhhhhhh.......eeee....hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee............eeeeee.........----hhhhhhheeeeeeeeeeeeee.....hhhhhhhhh..hhhhh.hhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhheeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nkv C   1 mDIPRIFTISESEHRIHNPFTEEKYATLGRVLRmKPGTRILDLGSGSGEmLCTWARDHGITGTGIDmSSLFTAQAKRRAEELGVSERVHFIHNDAAGYVANEKCDVAACVGATWIAGG----EELLAQSLKPGGImLIGEPYWRQLPATEEIAQACGVSSTSDFLTLPGLVGAFDDLGYDVVEmVLADQEGWDRYEAAKWLTmRRWLEANPDDDFAAEVRAELNIAPKRYVTYARECFGWGVFALIARLEHHH 253
                            |       10        20        30   |    40        50        60      | 70        80        90       100       110       | -  |    130     | 140       150       160       170       180   |   190       200  |    210       220       230       240       250   
                            1-MSE                           34-MSE          50-MSE           67-MSE                                            118  123          136-MSE                                         184-MSE            203-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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (YJHP_ECOLI | P39367)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1nkv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nkv)
 

(-) 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 ](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
  1nkv
    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
  YJHP_ECOLI | P39367
    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
  YJHP_ECOLI | P39367
    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 1NKV)

(-) Related Entries Specified in the PDB File

er13