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(-) Description

Title :  THIOCYANATE DEHYDROGENASE FROM THIOALKALIVIBRIO PARADOXUS
 
Authors :  A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, S. I. Tsallagov, I. G. Sh A. N. Popov, V. O. Popov
Date :  02 Dec 15  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Oxidoreductase, Thiocyanate Dehydrogenase, Copper Centers (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, S. I. Tsallagov, I. G. Shabalin, A. N. Popov, V. O. Popov
Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOCYANATE DEHYDROGENASE
    Chains: A, B, C, D
    Organism Scientific: THIOALKALIVIBRIO THIOCYANOXIDANS ARH 4
    Organism Taxid: 713587

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2CU8Ligand/IonCOPPER (II) ION
3GOL2Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CU-1Ligand/IonCOPPER (II) ION
3GOL1Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CU-1Ligand/IonCOPPER (II) ION
3GOL1Ligand/IonGLYCEROL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:206 , ASP A:314 , HIS A:381 , ACT A:603 , ACT A:604 , HOH A:757binding site for residue CU A 601
02AC2SOFTWARELYS A:103 , HIS A:135 , HIS A:528 , ACT A:604 , HOH A:702 , HOH A:830binding site for residue CU A 602
03AC3SOFTWAREHIS B:206 , ASP B:314 , HIS B:381 , ACT B:603 , ACT B:604 , HOH B:705binding site for residue CU B 601
04AC4SOFTWARELYS B:103 , HIS B:135 , HIS B:528 , ACT B:604 , HOH B:702 , HOH B:918binding site for residue CU B 602
05AC5SOFTWAREHIS C:206 , ASP C:314 , HIS C:381 , ACT C:603 , ACT C:604 , HOH C:744binding site for residue CU C 601
06AC6SOFTWARELYS C:103 , HIS C:135 , HIS C:136 , HIS C:528 , ACT C:604 , HOH C:702 , HOH C:801binding site for residue CU C 602
07AC7SOFTWAREMET C:451 , TRP C:453 , PRO C:458 , ASN C:459 , GLY C:460 , GLU C:474 , VAL C:475 , ASP C:476 , HOH C:714 , GLY D:272 , HOH D:735binding site for residue GOL C 605
08AC8SOFTWAREHIS D:206 , ASP D:314 , HIS D:381 , ACT D:603 , ACT D:604 , HOH D:767binding site for residue CU D 601
09AC9SOFTWARELYS D:103 , HIS D:135 , HIS D:528 , ACT D:604 , HOH D:801binding site for residue CU D 602
10AD1SOFTWAREHIS D:136 , HIS D:206 , HIS D:381 , HIS D:437 , CU D:601 , ACT D:604 , GOL D:606 , HOH D:767 , HOH D:796binding site for residue ACT D 603
11AD2SOFTWAREHIS D:135 , HIS D:136 , HIS D:206 , GLU D:288 , CU D:601 , CU D:602 , ACT D:603 , HOH D:801 , HOH D:1030binding site for residue ACT D 604
12AD3SOFTWAREASP D:243binding site for residue ACT D 605
13AD4SOFTWAREPRO D:291 , PHE D:436 , HIS D:437 , TRP D:452 , MET D:481 , HIS D:482 , ACT D:603 , HOH D:701 , HOH D:781 , HOH D:825 , HOH D:863 , HOH D:883binding site for residue GOL D 606
14AD5SOFTWAREASN D:410 , THR D:416 , HOH D:877 , HOH D:978binding site for residue PEG D 607
15AD6SOFTWAREHIS A:135 , HIS A:136 , HIS A:206 , GLU A:288 , HIS A:381 , HIS A:437 , CU A:601 , CU A:602 , HOH A:702 , HOH A:757 , HOH A:775 , HOH A:830binding site for residues ACT A 603 and ACT A 604
16AD7SOFTWAREHIS A:135 , HIS A:136 , HIS A:206 , GLU A:288 , HIS A:381 , HIS A:437 , CU A:601 , CU A:602 , HOH A:702 , HOH A:757 , HOH A:775 , HOH A:830binding site for residues ACT A 603 and ACT A 604
17AD8SOFTWAREHIS B:135 , HIS B:136 , HIS B:206 , ASP B:314 , HIS B:381 , HIS B:437 , CU B:601 , CU B:602 , HOH B:702 , HOH B:723 , HOH B:918binding site for residues ACT B 603 and ACT B 604
18AD9SOFTWAREHIS B:135 , HIS B:136 , HIS B:206 , ASP B:314 , HIS B:381 , HIS B:437 , CU B:601 , CU B:602 , HOH B:702 , HOH B:723 , HOH B:918binding site for residues ACT B 603 and ACT B 604
19AE1SOFTWAREHIS C:135 , HIS C:136 , HIS C:206 , GLU C:288 , HIS C:381 , HIS C:437 , CU C:601 , CU C:602 , HOH C:702 , HOH C:744 , HOH C:801 , HOH C:806binding site for residues ACT C 603 and ACT C 604
20AE2SOFTWAREHIS C:135 , HIS C:136 , HIS C:206 , GLU C:288 , HIS C:381 , HIS C:437 , CU C:601 , CU C:602 , HOH C:702 , HOH C:744 , HOH C:801 , HOH C:806binding site for residues ACT C 603 and ACT C 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F30)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:432 -Pro A:433
2Ser A:455 -Pro A:456
3Tyr B:432 -Pro B:433
4Ser B:455 -Pro B:456
5Tyr C:432 -Pro C:433
6Ser C:455 -Pro C:456
7Tyr D:432 -Pro D:433
8Ser D:455 -Pro D:456

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F30)

(-) Exons   (0, 0)

(no "Exon" information available for 5F30)

(-) 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeee.hhh.eeeeee.....eeeeee.hhhh....eeeeeee.........eeeeeeee.hhhhhh............eeeeeeeee....eeeeeehhhhhh......eee.....eeeeee....eeeeee.....eeeeeeeeeee............eeeeeee....hhhhh.................hhhhhhhh......hhhhh..eeeeee.....eeeeee....eeeeee....eeeeeee.......ee.eeeee..eeeeee......eeeeee.....eeeeee.....eeeeee.....hhhhheeeeee.hhhhh........eee.....eeeeee.......eeeeeee....eeeeeeeee..eeeeee.....eeeeeee.hhh..eeeeeee.....eeeeee........ee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f30 A  82 KYVKVQDFYDQLGKYVLVAPGKFSGTVAATDLSTGWTMAWLAAWNYGDTCPIMHHMAAFPSPDPYKEFEFVVNTQGGKNLFIYGVPVTVEDPGEGMKIYRIKYDGTRMNLQRDAAEVSGLGLGVHVTITPEADGYAVGDGQKDICAEFDRETDMVRYAWAFDWDPNVKDLKRAWLDGGTMTIKRLKPTLPGGRYDLQGSKGNKIDWELVPGGELAIEDGKVSGDRPLHSVANDALVFDPRGKWAVASMRLPGVCVVFDRENQVPVAVLAGPKGTPSQFQLVKVDDDTWTVDIPEVISAGHQAGFSPDGQSFLFMNSLRQNNIMVWDSSNHDDPTTWEKKAVVESPDWRGAYPNTFHMVFTPDAKKIYVTMWWPSPTPNGIAVIDAVNWEVLKEVDLGPDMHTLAITYDGKFVVGTLSGYQNTASAIVVMETETDEVLGFLPSPMGHHDNVIVPRTLEDLRISRSTTT 548
                                    91       101       111       121       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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       


Chain B from PDB  Type:PROTEIN  Length:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....eeeee.hhh.eeeeee.....eeeeee.hhhh....eeeeeee.........eeeeeeee.hhhhhh............eeeeeeeee....eeeeeehhhhhh......eee.....eeeeee....eeeeee.....eeeeeeeeeee............eeeeeee....hhhhh.................hhhhhhhh......hhhhh..eeeeee.....eeeeee....eeeeee....eeeeeee.......ee.eeeee..eeeeee......eeeeee.....eeeeee.....eeeeee.....hhhhheeeeee..............eee.....eeeeee.......eeeeeee....eeeeeeeee..eeeeee.....eeeeeee.hhh..eeeeeee.....eeeeee........ee...hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f30 B  82 KYVKVQDFYDQLGKYVLVAPGKFSGTVAATDLSTGWTMAWLAAWNYGDTCPIMHHMAAFPSPDPYKEFEFVVNTQGGKNLFIYGVPVTVEDPGEGMKIYRIKYDGTRMNLQRDAAEVSGLGLGVHVTITPEADGYAVGDGQKDICAEFDRETDMVRYAWAFDWDPNVKDLKRAWLDGGTMTIKRLKPTLPGGRYDLQGSKGNKIDWELVPGGELAIEDGKVSGDRPLHSVANDALVFDPRGKWAVASMRLPGVCVVFDRENQVPVAVLAGPKGTPSQFQLVKVDDDTWTVDIPEVISAGHQAGFSPDGQSFLFMNSLRQNNIMVWDSSNHDDPTTWEKKAVVESPDWRGAYPNTFHMVFTPDAKKIYVTMWWPSPTPNGIAVIDAVNWEVLKEVDLGPDMHTLAITYDGKFVVGTLSGYQNTASAIVVMETETDEVLGFLPSPMGHHDNVIVPRTLEDLRISRSTTT 548
                                    91       101       111       121       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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       


Chain C from PDB  Type:PROTEIN  Length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeee.hhh.eeeeee.....eeeeee.hhhh....eeeeeee.........eeeeeeee.hhhhhh............eeeeeeeee....eeeeeehhhhhh......eee.....eeeeee....eeeeee.....eeeeeeeeeee............eeeeeee....hhhhh.................hhhhhhhh......hhhhh..eeeeee.....eeeeee....eeeeee....eeeeeee.......ee.eeeee..eeeeee......eeeeee.....eeeeee.....eeeeee.....hhhhheeeeee..............eee.....eeeeee.......eeeeeee....eeeeeeeee..eeeeee.....eeeeeee.hhh..eeeeeee.....eeeeee........ee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f30 C  83 YVKVQDFYDQLGKYVLVAPGKFSGTVAATDLSTGWTMAWLAAWNYGDTCPIMHHMAAFPSPDPYKEFEFVVNTQGGKNLFIYGVPVTVEDPGEGMKIYRIKYDGTRMNLQRDAAEVSGLGLGVHVTITPEADGYAVGDGQKDICAEFDRETDMVRYAWAFDWDPNVKDLKRAWLDGGTMTIKRLKPTLPGGRYDLQGSKGNKIDWELVPGGELAIEDGKVSGDRPLHSVANDALVFDPRGKWAVASMRLPGVCVVFDRENQVPVAVLAGPKGTPSQFQLVKVDDDTWTVDIPEVISAGHQAGFSPDGQSFLFMNSLRQNNIMVWDSSNHDDPTTWEKKAVVESPDWRGAYPNTFHMVFTPDAKKIYVTMWWPSPTPNGIAVIDAVNWEVLKEVDLGPDMHTLAITYDGKFVVGTLSGYQNTASAIVVMETETDEVLGFLPSPMGHHDNVIVPRTLEDLRISRSTTT 548
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542      


Chain D from PDB  Type:PROTEIN  Length:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....eeeee.hhh.eeeeee.....eeeeee.hhhh....eeeeeee.........eeeeeeee.hhhhhh............eeeeeeeee....eeeeeehhhhhh......eee.....eeeeee....eeeeee.....eeeeeeeeeee............eeeeeee....hhhhh.................hhhhhhhh......hhhhh..eeeeee.....eeeeee....eeeeee....eeeeeee.......ee.eeeee..eeeeee......eeeeee.....eeeeee.....eeeeee.....hhhhheeeeee..............eee.....eeeeee.......eeeeeee....eeeeeeeee..eeeeee.....eeeeeee.hhh..eeeeeee.....eeeeee........ee...hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f30 D  82 KYVKVQDFYDQLGKYVLVAPGKFSGTVAATDLSTGWTMAWLAAWNYGDTCPIMHHMAAFPSPDPYKEFEFVVNTQGGKNLFIYGVPVTVEDPGEGMKIYRIKYDGTRMNLQRDAAEVSGLGLGVHVTITPEADGYAVGDGQKDICAEFDRETDMVRYAWAFDWDPNVKDLKRAWLDGGTMTIKRLKPTLPGGRYDLQGSKGNKIDWELVPGGELAIEDGKVSGDRPLHSVANDALVFDPRGKWAVASMRLPGVCVVFDRENQVPVAVLAGPKGTPSQFQLVKVDDDTWTVDIPEVISAGHQAGFSPDGQSFLFMNSLRQNNIMVWDSSNHDDPTTWEKKAVVESPDWRGAYPNTFHMVFTPDAKKIYVTMWWPSPTPNGIAVIDAVNWEVLKEVDLGPDMHTLAITYDGKFVVGTLSGYQNTASAIVVMETETDEVLGFLPSPMGHHDNVIVPRTLEDLRISRSTTT 548
                                    91       101       111       121       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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541
   Legend:   → Mismatch (orange background)
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  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 5F30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F30)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F30)

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  5f30
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        W0DP94_9GAMM | W0DP94: 5f75

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