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

(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN NE0167 FROM NITROSOMONAS EUROPAEA
 
Authors :  C. Chang, E. Evdokimova, A. Savchenko, A. M. Edwards, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)
Date :  08 Oct 09  (Deposition) - 27 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Structural Genomics, Mcsg, Unknown Function Protein, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, E. Evdokimova, A. Savchenko, A. M. Edwards, A. Joachimiak
Crystal Structure Of Protein Ne0167 From Nitrosomonas Europaea
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN NE0167
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Gene: NE0167
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 915
    Strain: ATCC 19718

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric/Biological Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K6C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K6C)

(-) Exons   (0, 0)

(no "Exon" information available for 3K6C)

(-) 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:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6ca_ A: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c A  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:90
                                    13        23        33        43        53        63        73        83        93
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIA 93
               SCOP domains d3k6cb_ B: Hypothetical protein NE0167                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  3k6c B  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIA 93
                                    13      | 23        33        43        53        63  |     73        83        93
                                           20-MSE                                        66-MSE                       


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6cc_ C: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c C  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain D from PDB  Type:PROTEIN  Length:92
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAHE 95
               SCOP domains d3k6cd_ D: Hypothetical protein NE0167                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3k6c D  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAHE 95
                                    13      | 23        33        43        53        63  |     73        83        93  
                                           20-MSE                                        66-MSE                         


Chain E from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6ce_ E: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c E  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain F from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6cf_ F: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c F  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain G from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    12        22        32        42        52        62        72        82        92 
          Q82XT5_NITEU    3 NDGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIA 93
               SCOP domains d3k6cg_ G: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c G  3 NDGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIA 93
                                    12       |22        32        42        52        62   |    72        82        92 
                                            20-MSE                                        66-MSE                       


Chain H from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6ch_ H: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c H  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain I from PDB  Type:PROTEIN  Length:91
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:91
                                    13        23        33        43        53        63        73        83        93 
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
               SCOP domains d3k6ci_ I: Hypothetical protein NE0167                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3k6c I  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIAH 94
                                    13      | 23        33        43        53        63  |     73        83        93 
                                           20-MSE                                        66-MSE                        


Chain J from PDB  Type:PROTEIN  Length:90
 aligned with Q82XT5_NITEU | Q82XT5 from UniProtKB/TrEMBL  Length:95

    Alignment length:90
                                    13        23        33        43        53        63        73        83        93
          Q82XT5_NITEU    4 DGYFEPTQELSDETRDMHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAMLLEWIRRCDPAFDKELKDYLFTNKPIA 93
               SCOP domains d3k6cj_ J: Hypothetical protein NE0167                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  3k6c J  4 DGYFEPTQELSDETRDmHRAIISLREELEAVDLYNQRVNACKDKELKAILAHNRDEEKEHAAmLLEWIRRCDPAFDKELKDYLFTNKPIA 93
                                    13      | 23        33        43        53        63  |     73        83        93
                                           20-MSE                                        66-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, 10)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K6C)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3K6C)

 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 3k6c)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3k6c)
 

(-) 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
  3k6c
    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
  Q82XT5_NITEU | Q82XT5
    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
  Q82XT5_NITEU | Q82XT5
    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 3K6C)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K6C)