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(-) Description

Title :  CRYSTAL STRUCTURE OF ATPASE-TYPE HYPB IN THE NUCLEOTIDE FREE STATE
 
Authors :  S. Watanabe, T. Kawashima, Y. Nishitani, K. Miki
Date :  27 May 15  (Deposition) - 24 Jun 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,F  (1x)
Keywords :  Atpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Watanabe, T. Kawashima, Y. Nishitani, T. Kanai, T. Wada, K. Inaba, H. Atomi, T. Imanaka, K. Miki
Structural Basis Of A Ni Acquisition Cycle For [Nife] Hydrogenase By Ni-Metallochaperone Hypa And Its Enhancer
Proc. Natl. Acad. Sci. Usa V. 112 7701 2015
PubMed-ID: 26056269  |  Reference-DOI: 10.1073/PNAS.1503102112

(-) Compounds

Molecule 1 - ATPASE INVOLVED IN CHROMOSOME PARTITIONING, PARA/MIND FAMILY, MRP HOMOLOG
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK2007
    Organism Scientific: THERMOCOCCUS KODAKARAENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
    Synonym: HYPB

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A      H
Biological Unit 2 (1x):  B  E   
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D F  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , GLU A:125 , HOH A:405 , ALA D:13 , GLU D:16binding site for residue GOL A 301
2AC2SOFTWAREARG B:14 , GLU B:16 , GLY B:17 , ARG B:122 , ASP B:124 , GLU B:125 , ALA C:13binding site for residue GOL B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AUQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AUQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AUQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AUQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5AUQ)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhhh................ee..eeeee.hhh..hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhh...eeeeee...hhhhhh.hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq A   4 IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLRKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    13        23        33        43        53        63        73        83        93    || 109       119       129       139       149       159       169       179       189 ||    206       216       226       236       246  
                                                                                                                         98|                                                                                   191|                                                 
                                                                                                                         105                                                                                    199                                                 


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh.................eeeee.hhh...hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhh...eeeeee...hhhhhh.hhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq B   5 DPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPGVVPPTVHGIKFMTIAYYTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    14        24        34        44        54        64        74||      88        98|      113       123       133       143       153       163       173       183      |201       211       221       231       241       
                                                                                                 75|                98|                                                                                   190|                                                 
                                                                                                  80                104                                                                                    199                                                 


Chain C from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhhh................ee..eeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhh...eeeeee.hhhhhhhh.hhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq C   5 DPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    14        24        34        44        54        64        74        84        94   ||  109       119       129       139       149       159       169       179       189||     208       218       228       238       248
                                                                                                                        98|                                                                                   190|                                                
                                                                                                                        104                                                                                    200                                                


Chain D from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhh................ee..eeeee.hhh...hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhh...eeeeee...hhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq D   5 DPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    14        24        34        44        54        64        74        84        94   ||  109       119       129       139       149       159       169       179       189||     207       217       227       237       247 
                                                                                                                        98|                                                                                   190|                                                 
                                                                                                                        104                                                                                    199                                                 


Chain E from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhh.......ee..eeeee.hhh..hhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhh...eeeeee...hhhhhh.hhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq E   7 REIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPVVPPTVHGIKFMTIAYYTLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    16        26        36        46        56        66    ||  85        95  ||   111       121       131       141       151       161       171       181       200       210       220       230       240        
                                                                                           71|               98|                                                                                  190|                                                
                                                                                            81               105                                                                                   200                                                


Chain F from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhh.............ee..eeeee.hhh..hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhh...eeeeee....hhhhh.hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq F   7 REIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEGVVPPTVHGIKFMTIAYYTLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    16        26        36        46        56        66        76|       89       105       115       125       135       145       155       165       175       185    || 203       213       223       233       243     
                                                                                                76|                98|                                                                                  190|                                                 
                                                                                                 80                105                                                                                   199                                                 


Chain G from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh.................ee..eeeee.hhhh.hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhh...eeeeee..........hhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq G   5 DPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    14        24        34        44        54        64        74        84        94   ||  110       120       130       140       150       160       170       180       190|      208       218       228       238       248
                                                                                                                        98|                                                                                  190|                                                 
                                                                                                                        105                                                                                   199                                                 


Chain H from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhh..............ee..eeeee.hhh...hhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhh...eeeeee...hhhhhh.hhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5auq H   5 DPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGLLDLDFHGASDHVILGFEPKEFPEGVVPPTVHGIKFMTIAYYTPLRGKEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVATPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLREKDVEKLAEEFGVPYLVGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL 248
                                    14        24        34        44        54        64        74 ||     87        97||     112       122       132       142       152       162       172       182       198       208       218       228       238       248
                                                                                                  76|                98|                                                                                    191|                                                  
                                                                                                   80                104                                                                                     198
   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  (0, 0)

(no "SCOP Domain" information available for 5AUQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AUQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AUQ)

(-) Gene Ontology  (6, 6)

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  5auq
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  Q5JIH4_THEKO | Q5JIH4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5JIH4_THEKO | Q5JIH4: 3vx3 5aun 5auo 5aup

(-) Related Entries Specified in the PDB File

3vx3 3VX3 CONTAINS THE SAME PROTEIN COMPLEXED WITH ADP.
5aun
5auo
5aup