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
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PH0347 PROTEIN FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  N. K. Lokanath, Y. Terao, N. Kunishima, Riken Structural Genomics/P Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 15 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hypothetical Proteins, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, Y. Terao, N. Kunishima
Crystal Structure Of Ph0347 Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 177AA LONG HYPOTHETICAL PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: 21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1NI6Ligand/IonNICKEL (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , HIS A:67 , ASP A:68 , ASP A:124BINDING SITE FOR RESIDUE NI A 601
2AC2SOFTWAREHIS B:33 , HIS B:67 , ASP B:68 , ASP B:124BINDING SITE FOR RESIDUE NI B 602
3AC3SOFTWAREHIS C:33 , HIS C:67 , ASP C:68 , ASP C:124BINDING SITE FOR RESIDUE NI C 603
4AC4SOFTWAREHIS D:33 , HIS D:67 , ASP D:68 , ASP D:124BINDING SITE FOR RESIDUE NI D 604
5AC5SOFTWAREHIS E:33 , HIS E:67 , ASP E:68 , ASP E:124BINDING SITE FOR RESIDUE NI E 605
6AC6SOFTWAREHIS F:33 , HIS F:67 , ASP F:68 , ASP F:124BINDING SITE FOR RESIDUE NI F 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CQZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CQZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CQZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CQZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2CQZ)

(-) 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:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqza_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzA00 A:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz A   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqzb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzB00 B:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz B   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqzc_ C: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzC00 C:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz C   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqzd_ D: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzD00 D:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz D   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain E from PDB  Type:PROTEIN  Length:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqze_ E: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzE00 E:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz E   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain F from PDB  Type:PROTEIN  Length:173
 aligned with O58085_PYRHO | O58085 from UniProtKB/TrEMBL  Length:177

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O58085_PYRHO     4 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 176
               SCOP domains d2cqzf_ F: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2cqzF00 F:1-173 Hypothetical protein af1432                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cqz F   1 MIEKILLVQTLKRLPRMGWLIKGVQEPESIADHSFGVAFITLVLADVLEKRGKRIDVEKALKMAIVHDLAEAIITDIPLSAQEFVDKDKAEALVFKKVFPEFYELYREYQECSSPEAQLVRIADKLDMILQAYQYELSGNKNLDEFWEAIEEIKRLELSKYLEDILNSVGRLK 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CQZ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2CQZ)

 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
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cqz)
 

(-) 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 | Asym./Biol. Unit - sites 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
  2cqz
    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
  O58085_PYRHO | O58085
    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
  O58085_PYRHO | O58085
    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 2CQZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CQZ)