Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A SIGMA54-ACTIVATOR SUGGESTS THE MECHANISM FOR THE CONFORMATIONAL SWITCH NECESSARY FOR SIGMA54 BINDING
 
Authors :  L. Sallai, P. A. Tucker
Date :  10 Jul 03  (Deposition) - 19 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  D,E,F  (2x)
Keywords :  Response Regulator, Two Component System, Aaa Domain, Ntrc Family, Dna-Binding, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Sallai, P. A. Tucker
Crystal Structure Of The Central And C-Terminal Domain Of The Sigma(54)-Activator Zrar.
J. Struct. Biol. V. 151 160 2005
PubMed-ID: 16005641  |  Reference-DOI: 10.1016/J.JSB.2005.05.006

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: B834
    Expression System Taxid: 562
    Fragment: ATPASE (AAA) AND DNA BINDING DOMAINS, RESIDUES 141-441
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Other Details: N-TERMINAL(RECEIVER) DOMAIN DELETED
    Synonym: HYDG, ZRAR, STM4174, STMF1.27

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABC   
Biological Unit 2 (2x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:171 , GLY A:172 , THR A:173 , LYS A:175 , ARG A:359BINDING SITE FOR RESIDUE PO4 A1442
2AC2SOFTWARESER B:171 , GLY B:172 , THR B:173 , LYS B:175 , ARG B:359BINDING SITE FOR RESIDUE PO4 B1390
3AC3SOFTWAREASP C:170 , SER C:171 , GLY C:172 , THR C:173 , LYS C:175 , ARG C:359BINDING SITE FOR RESIDUE PO4 C1391
4AC4SOFTWARESER D:171 , GLY D:172 , THR D:173 , LYS D:175 , ARG D:359BINDING SITE FOR RESIDUE PO4 D1442
5AC5SOFTWARESER F:171 , GLY F:172 , THR F:173 , LYS F:175 , GLU F:176 , ASP F:240 , ARG F:359BINDING SITE FOR RESIDUE PO4 F1390
6AC6SOFTWAREILE E:142 , SER E:171 , GLY E:172 , THR E:173 , GLY E:174 , LYS E:175 , GLU E:176 , ASP E:240 , ARG E:315 , LEU E:322 , PHE E:326 , ARG E:329 , ILE E:358 , ARG E:359 , GLU E:362BINDING SITE FOR RESIDUE ATP E1442

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 24)

Asymmetric Unit (4, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIGMA54_INTERACT_4PS50045 Sigma-54 interaction domain profile.ZRAR_SALTY141-370
 
 
 
 
 		  6A:141-370
B:141-370
C:141-370
D:141-370
E:141-370
F:141-370
2SIGMA54_INTERACT_1PS00675 Sigma-54 interaction domain ATP-binding region A signature.ZRAR_SALTY165-178
 
 
 
 
 		  6A:165-178
B:165-178
C:165-178
D:165-178
E:165-178
F:165-178
3SIGMA54_INTERACT_2PS00676 Sigma-54 interaction domain ATP-binding region B signature.ZRAR_SALTY227-242
 
 
 
 
 		  6A:227-242
B:227-242
C:227-242
D:227-242
E:227-242
F:227-242
4SIGMA54_INTERACT_3PS00688 Sigma-54 interaction domain C-terminal part signature.ZRAR_SALTY354-363
 
 
 
 
 		  6A:354-363
B:354-363
C:354-363
D:354-363
E:354-363
F:354-363
Biological Unit 1 (4, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIGMA54_INTERACT_4PS50045 Sigma-54 interaction domain profile.ZRAR_SALTY141-370
 
 
 
 
 		  6A:141-370
B:141-370
C:141-370
-
-
-
2SIGMA54_INTERACT_1PS00675 Sigma-54 interaction domain ATP-binding region A signature.ZRAR_SALTY165-178
 
 
 
 
 		  6A:165-178
B:165-178
C:165-178
-
-
-
3SIGMA54_INTERACT_2PS00676 Sigma-54 interaction domain ATP-binding region B signature.ZRAR_SALTY227-242
 
 
 
 
 		  6A:227-242
B:227-242
C:227-242
-
-
-
4SIGMA54_INTERACT_3PS00688 Sigma-54 interaction domain C-terminal part signature.ZRAR_SALTY354-363
 
 
 
 
 		  6A:354-363
B:354-363
C:354-363
-
-
-
Biological Unit 2 (4, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIGMA54_INTERACT_4PS50045 Sigma-54 interaction domain profile.ZRAR_SALTY141-370
 
 
 
 
 		  6-
-
-
D:141-370
E:141-370
F:141-370
2SIGMA54_INTERACT_1PS00675 Sigma-54 interaction domain ATP-binding region A signature.ZRAR_SALTY165-178
 
 
 
 
 		  6-
-
-
D:165-178
E:165-178
F:165-178
3SIGMA54_INTERACT_2PS00676 Sigma-54 interaction domain ATP-binding region B signature.ZRAR_SALTY227-242
 
 
 
 
 		  6-
-
-
D:227-242
E:227-242
F:227-242
4SIGMA54_INTERACT_3PS00688 Sigma-54 interaction domain C-terminal part signature.ZRAR_SALTY354-363
 
 
 
 
 		  6-
-
-
D:354-363
E:354-363
F:354-363

(-) Exons   (0, 0)

(no "Exon" information available for 1OJL)

(-) 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:292
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:302
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
           ZRAR_SALTY   140 GMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATPIKTEYSGEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ojlA01 A:140-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                      1ojlA02 A:312-387  [code=1.10.8.60, no name defined]                               1ojlA03 A:395-441 Homeodomain-like              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh........eee....hhhhhhhhhh........---....hhhhhhh..eeeee.....hhhhhhhhhhhhhh................eeeeee..hhhhhhhhh..hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh-------......hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SIGMA54_INTERACT_4  PDB: A:141-370 UniProt: 141-370                                                                                                                                                                                   ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl A 140 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFT---KRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIA-------YSGEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
                                   149       159       169       179       189       199       209       219   |   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       | -     | 399       409       419       429       439  
                                                                                                         219 223                                                                                                                                                                 387     395                                              


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:268
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
           ZRAR_SALTY   122 AHTRETGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAAT 389
               SCOP domains d1                 ojlb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 1o                 jlB01 B:139-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                        1ojlB02 B:313-389  [code=1.10.8.60, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh........eee....hhhhhhhhhh...............hhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh.ee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------SIGMA54_INTERACT_4  PDB: B:141-370 UniProt: 141-370                                                                                                                                                                                   ------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN-------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl B 139 SH-----------------MIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAAT 389
                             |       -       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
                           140               141                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:269
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
           ZRAR_SALTY   122 AHTRETGAELPSASAAQFGMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATP 390
               SCOP domains d1                 ojlc_ C: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1o                 jlC01 C:139-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                        1ojlC02 C:313-390  [code=1.10.8.60, no name defined]                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh......eeeee....hhhhhhhhhh...............hhhhhhh..eeeee.....hhhhhhhhhhhhhh................eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------SIGMA54_INTERACT_4  PDB: C:141-370 UniProt: 141-370                                                                                                                                                                                   -------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN--------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl C 139 SH-----------------MIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATP 390
                             |       -       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                           140               141                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:297
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:302
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
           ZRAR_SALTY   140 GMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATPIKTEYSGEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ojlD01 D:140-310 P-loop containing nucleotide triphosphate hydrolases                                                                                                     1ojlD02 D:311-392  [code=1.10.8.60, no name defined]                              -----1ojlD03 D:398-441 Homeodomain-like           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh......eeeee....hhhhhhhhhh.................hhhhh..eeeee.....hhhhhhhhhhhhhh.ee........ee...eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.....-----...hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SIGMA54_INTERACT_4  PDB: D:141-370 UniProt: 141-370                                                                                                                                                                                   ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl D 140 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATPIK-----EIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389  |    399       409       419       429       439  
                                                                                                                                                                                                                                                                                      392   398                                           


Chain E from PDB  Type:PROTEIN  Length:285
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:302
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
           ZRAR_SALTY   140 GMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAATPIKTEYSGEIQPLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----1ojlE01 E:145-311 P-loop containing nucleotide triphosphate hydrolases                                                                                                 1ojlE02 E:312-386  [code=1.10.8.60, no name defined]                                     1ojlE03 E:401-441 Homeodomain-like        CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_8-1ojlE01 E:401-441                   Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_8-1ojlE02 E:401-441                   Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_8-1ojlE03 E:401-441                   Pfam domains (3)
         Sec.struct. author ......hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh......eeeee....hhhhhhhhhh........---......hhhhh.eeeeee.....hhhhhhhhhhhhhh...............eeeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhh....--------------hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SIGMA54_INTERACT_4  PDB: E:141-370 UniProt: 141-370                                                                                                                                                                                   ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl E 140 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFT---KRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAI--------------PLVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
                                   149       159       169       179       189       199       209       219   |   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      |  -         - |     409       419       429       439  
                                                                                                         219 223                                                                                                                                                                386            401                                        


Chain F from PDB  Type:PROTEIN  Length:247
 aligned with ZRAR_SALTY | P25852 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:250
                                   149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
           ZRAR_SALTY   140 GMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAAT 389
               SCOP domains d1ojlf_ F: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ojlF01 F:140-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                       1ojlF02 F:313-389  [code=1.10.8.60, no name defined]                          CATH domains
           Pfam domains (1) -Sigma54_activat-1ojlF01 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Sigma54_activat-1ojlF02 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -Sigma54_activat-1ojlF03 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -Sigma54_activat-1ojlF04 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -Sigma54_activat-1ojlF05 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) -Sigma54_activat-1ojlF06 F:141-308                                                                                                                                       --------------------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author .....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh........eee....hhhhhhhhhh........---......hhhhh..eeeee.hhhhhhhhhhhhhhhhhh................eeeeee..hhhhhhhh...hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SIGMA54_INTERACT_4  PDB: F:141-370 UniProt: 141-370                                                                                                                                                                                   ------------------- PROSITE (1)
                PROSITE (2) -------------------------SIGMA54_INTERA------------------------------------------------SIGMA54_INTERACT---------------------------------------------------------------------------------------------------------------SIGMA54_IN-------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ojl F 140 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFGHEKGAFT---KRREGRFVEADGGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLLTGEYISERELPLAIAAT 389
                                   149       159       169       179       189       199       209       219   |   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
                                                                                                         219 223
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 15)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 9)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Family: HTH_8 (10)
(-)
Salmonella typhimurium (1)
1aHTH_8-1ojlE01E:401-441
1bHTH_8-1ojlE02E:401-441
1cHTH_8-1ojlE03E:401-441
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ZRAR_SALTY | P25852)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 1ojl)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1ojl
    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
  ZRAR_SALTY | P25852
    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
  ZRAR_SALTY | P25852
    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 1OJL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1OJL)