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(-) Description

Title :  STRUCTURE OF PH1012 PROTEIN FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Dec 05  (Deposition) - 28 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Hypothetical Protein, X-Ray Diffraction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, N. Kunishima
Crystal Structure Of Ph1012 Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 165AA LONG HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PH1012
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: PH1012 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:6 , LEU A:158 , TYR A:159BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWAREARG A:45 , ARG A:102 , CL A:503BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREARG A:45 , ARG A:47 , LYS A:100 , ARG A:102 , TYR A:159 , CL A:502 , HOH A:518BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWAREARG B:45 , ARG B:47 , ARG B:102 , CL B:505BINDING SITE FOR RESIDUE CL B 504
5AC5SOFTWAREARG B:47 , LYS B:100 , ARG B:102 , TYR B:159 , CL B:504 , HOH B:519BINDING SITE FOR RESIDUE CL B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DC4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:40 -Pro A:41
2Ser B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DC4)

(-) Exons   (0, 0)

(no "Exon" information available for 2DC4)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:164
 aligned with O58740_PYRHO | O58740 from UniProtKB/TrEMBL  Length:165

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         O58740_PYRHO     1 MEIEVKFRVNFEDIKRKIEGLGAKFFGIEEQEDVYFELPSPKLLRVRKINNTGKSYITYKEILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKRRWIYKLNNVTFELNRVEKAGDFLDIEVITSNPEEGKKIIWDVARRLGLKEEDVEPKLYIELIN 164
               SCOP domains d2dc4a_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains 2dc4A00 A:1-164 Hypothetical Protein Pfu-838710-001                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhh.eeeeeeeeeeeee.....eeeeeeee.....eeeeeeee......eeeeeeee..hhhhhhhhhhhh...eeeeeeeeeeeeee..eeeeeeee...eeeeeeee...hhhhhhhhhhhhhhhh..hhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dc4 A   1 MEIEVKFRVNFEDIKRKIEGLGAKFFGIEEQEDVYFELPSPKLLRVRKINNTGKSYITYKEILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKRRWIYKLNNVTFELNRVEKAGDFLDIEVITSNPEEGKKIIWDVARRLGLKEEDVEPKLYIELIN 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with O58740_PYRHO | O58740 from UniProtKB/TrEMBL  Length:165

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         O58740_PYRHO     1 MEIEVKFRVNFEDIKRKIEGLGAKFFGIEEQEDVYFELPSPKLLRVRKINNTGKSYITYKEILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKRRWIYKLNNVTFELNRVEKAGDFLDIEVITSNPEEGKKIIWDVARRLGLKEEDVEPKLYIELIN 164
               SCOP domains d2dc4b_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains 2dc4B00 B:1-164 Hypothetical Protein Pfu-838710-001                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeeee.....eeeeeeee......eeeeeeee..hhhhhhhhhhhh...eeeeeeeeeeeeee..eeeeeeee...eeeeeeee...hhhhhhhhhhhhhhhh..hhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dc4 B   1 MEIEVKFRVNFEDIKRKIEGLGAKFFGIEEQEDVYFELPSPKLLRVRKINNTGKSYITYKEILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKRRWIYKLNNVTFELNRVEKAGDFLDIEVITSNPEEGKKIIWDVARRLGLKEEDVEPKLYIELIN 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DC4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2DC4)

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