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(-) Description

Title :  CRYSTAL STRUCTURE OF NICOTINATE DEHYDROGENASE
 
Authors :  N. Wagener, A. J. Pierik, R. Hille, H. Dobbek
Date :  09 Jun 09  (Deposition) - 30 Jun 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Selenium Ligand, 2Fe-2S, Iron, Iron-Sulfur, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Wagener, A. J. Pierik, A. Ibdah, R. Hille, H. Dobbek
The Mo-Se Active Site Of Nicotinate Dehydrogenase
Proc. Natl. Acad. Sci. Usa V. 106 11055 2009
PubMed-ID: 19549881  |  Reference-DOI: 10.1073/PNAS.0902210106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINATE DEHYDROGENASE LARGE MOLYBDOPTERIN SUBUNIT
    Chains: A, E
    Organism Common: CLOSTRIDIUM BARKERI
    Organism Scientific: EUBACTERIUM BARKERI
    Organism Taxid: 1528
 
Molecule 2 - NICOTINATE DEHYDROGENASE MEDIUM MOLYBDOPTERIN SUBUNIT
    Chains: B, F
    Organism Common: CLOSTRIDIUM BARKERI
    Organism Scientific: EUBACTERIUM BARKERI
    Organism Taxid: 1528
 
Molecule 3 - NICOTINATE DEHYDROGENASE FAD-SUBUNIT
    Chains: C, G
    Organism Common: CLOSTRIDIUM BARKERI
    Organism Scientific: EUBACTERIUM BARKERI
    Organism Taxid: 1528
 
Molecule 4 - NICOTINATE DEHYDROGENASE SMALL FES SUBUNIT
    Chains: D, H
    Organism Common: CLOSTRIDIUM BARKERI
    Organism Scientific: EUBACTERIUM BARKERI
    Organism Taxid: 1528

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 20)

Asymmetric/Biological Unit (9, 20)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3FES4Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4MCN2Ligand/IonPTERIN CYTOSINE DINUCLEOTIDE
5MG2Ligand/IonMAGNESIUM ION
6MOS2Ligand/IonDIOXOTHIOMOLYBDENUM(VI) ION
7NIO2Ligand/IonNICOTINIC ACID
8NO33Ligand/IonNITRATE ION
9SE2Ligand/IonSELENIUM ATOM

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:239 , GLY A:240 , ALA A:349 , PHE A:350 , ARG A:351 , GLU B:289 , MOS B:920 , MCN B:921BINDING SITE FOR RESIDUE SE A 922
02AC2SOFTWAREARG A:278 , HIS A:279 , VAL A:316 , GLY A:348 , ALA A:349 , PHE A:350 , PHE A:353 , GLY A:354 , GLN A:357BINDING SITE FOR RESIDUE NO3 A 5658
03AC3SOFTWARETHR A:207 , ASN A:209 , ASP A:213 , LYS A:242 , LEU A:243 , ASP A:244 , GLN A:248 , HOH A:448BINDING SITE FOR RESIDUE MG A 426
04AC4SOFTWARETHR A:306 , TYR A:309 , ALA A:310 , SER A:347BINDING SITE FOR RESIDUE MG A 427
05AC5SOFTWAREGLN A:208 , GLY A:240 , LEU A:243 , PHE A:353 , SE A:922 , THR B:84 , SER B:85 , ALA B:86 , GLU B:289 , MCN B:921BINDING SITE FOR RESIDUE MOS B 920
06AC6SOFTWAREGLY A:237 , GLY A:238 , PHE A:239 , ARG A:351 , SE A:922 , ILE B:45 , GLY B:46 , GLN B:47 , GLY B:48 , SER B:49 , THR B:84 , SER B:85 , ALA B:86 , SER B:87 , ARG B:88 , GLN B:89 , THR B:90 , VAL B:211 , THR B:213 , ILE B:215 , ASN B:216 , MET B:219 , VAL B:220 , GLN B:223 , ALA B:284 , LYS B:285 , GLY B:286 , VAL B:287 , GLY B:288 , GLU B:289 , HOH B:384 , HOH B:446 , MOS B:920 , GLN D:100 , CYS D:138BINDING SITE FOR RESIDUE MCN B 921
07AC7SOFTWARETYR A:312 , ALA A:315 , ARG A:319 , PHE A:353 , HOH A:513 , ASN B:17 , THR B:18 , LEU B:20BINDING SITE FOR RESIDUE NIO B 5661
08AC8SOFTWAREILE C:29 , ALA C:31 , GLY C:32 , GLY C:33 , THR C:34 , ASP C:35 , LEU C:36 , ILE C:38 , ALA C:73 , PHE C:77 , VAL C:100 , GLY C:101 , ILE C:105 , THR C:110 , GLY C:113 , ASN C:114 , SER C:116 , THR C:117 , GLY C:122 , ASP C:123 , ARG C:160 , ILE C:168 , MET C:169 , LYS C:187 , ALA C:195 , HOH C:303 , HOH C:329 , HOH C:359 , HOH C:361 , HOH C:388 , GLU D:44 , GLY D:45 , GLU D:46BINDING SITE FOR RESIDUE FAD C 900
09AC9SOFTWARECYS C:222 , ARG C:265 , PRO C:266 , SER C:267 , VAL C:268 , LYS C:271BINDING SITE FOR RESIDUE NO3 C 5659
10BC1SOFTWAREILE A:186 , GLN D:100 , CYS D:101 , GLY D:102 , CYS D:104 , CYS D:136 , ARG D:137 , CYS D:138BINDING SITE FOR RESIDUE FES D 907
11BC2SOFTWAREGLY D:41 , CYS D:42 , SER D:43 , GLY D:45 , GLU D:46 , CYS D:47 , GLY D:48 , CYS D:50 , THR D:60 , CYS D:62BINDING SITE FOR RESIDUE FES D 908
12BC3SOFTWAREPHE E:239 , GLY E:240 , ALA E:349 , PHE E:350 , ARG E:351 , GLU F:289 , MOS F:920 , MCN F:921BINDING SITE FOR RESIDUE SE E 922
13BC4SOFTWAREGLU A:198 , VAL E:15 , GLU E:19 , HOH E:441 , HOH E:757 , VAL F:70 , THR F:71 , TRP F:72BINDING SITE FOR RESIDUE NIO E 5660
14BC5SOFTWAREARG E:278 , HIS E:279 , VAL E:316 , GLY E:348 , ALA E:349 , PHE E:350 , GLY E:354 , GLN E:357BINDING SITE FOR RESIDUE NO3 E 5662
15BC6SOFTWARETHR E:207 , ASN E:209 , ASP E:213 , LYS E:242 , LEU E:243 , ASP E:244 , GLN E:248BINDING SITE FOR RESIDUE CA E 5663
16BC7SOFTWAREGLN E:208 , GLY E:240 , LEU E:243 , SE E:922 , THR F:84 , SER F:85 , ALA F:86 , GLU F:289 , MCN F:921BINDING SITE FOR RESIDUE MOS F 920
17BC8SOFTWAREGLY E:238 , PHE E:239 , ARG E:351 , SE E:922 , ILE F:45 , GLY F:46 , GLN F:47 , GLY F:48 , SER F:49 , THR F:84 , SER F:85 , ALA F:86 , SER F:87 , ARG F:88 , GLN F:89 , THR F:90 , VAL F:211 , THR F:213 , ILE F:215 , ASN F:216 , MET F:219 , VAL F:220 , GLN F:223 , ALA F:284 , LYS F:285 , GLY F:286 , VAL F:287 , GLY F:288 , GLU F:289 , HOH F:333 , HOH F:895 , MOS F:920 , GLN H:100 , CYS H:138BINDING SITE FOR RESIDUE MCN F 921
18BC9SOFTWAREILE G:29 , ALA G:31 , GLY G:32 , GLY G:33 , THR G:34 , ASP G:35 , LEU G:36 , ILE G:38 , ILE G:53 , PHE G:77 , VAL G:100 , GLY G:101 , ILE G:105 , THR G:110 , GLY G:113 , ASN G:114 , SER G:116 , THR G:117 , GLY G:122 , ASP G:123 , ARG G:160 , ILE G:168 , MET G:169 , LYS G:187 , ALA G:195 , HOH G:297 , GLU H:44 , GLY H:45 , GLU H:46BINDING SITE FOR RESIDUE FAD G 900
19CC1SOFTWAREILE E:186 , GLN H:100 , CYS H:101 , GLY H:102 , CYS H:104 , CYS H:136 , ARG H:137 , CYS H:138BINDING SITE FOR RESIDUE FES H 907
20CC2SOFTWAREGLY H:41 , CYS H:42 , SER H:43 , GLY H:45 , GLU H:46 , CYS H:47 , GLY H:48 , CYS H:50 , CYS H:62BINDING SITE FOR RESIDUE FES H 908

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HRD)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr B:314 -Pro B:315
2Val C:25 -Pro C:26
3Gly F:278 -Pro F:279
4Thr F:314 -Pro F:315
5Val G:25 -Pro G:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HRD)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.NDFS_EUBBA1-179
 		  2C:1-179
G:1-179
22FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.NDSFS_EUBBA4-80
 		  2D:4-80
H:4-80
32FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.NDSFS_EUBBA42-50
 		  2D:42-50
H:42-50

(-) Exons   (0, 0)

(no "Exon" information available for 3HRD)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:420
 aligned with NDLMS_EUBBA | Q0QLF2 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:420
                                    11        21        31        41        51        61        71        81        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
          NDLMS_EUBBA     2 GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARIVSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDAIAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIHQVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGMLTVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHCALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVEMFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFRGFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENSVGLIETLEKAREKAVEVMGY 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhh....hhhhh.....eeeeeee.....eeeeeeehhhhhh...eeeeehhhhh..........................eeeeeee.hhhhhhhhhhhheeeeee.....hhhhhhh...........eeeeeeeee.hhhhhhhh..eeeeeeeee...........eeeeee.....eeeee...hhhhhhhhhhhhh..hhh.eeeee..............hhhhhhhhhhhhh..eeee.hhhhhhhhh.....eeeeeeeee.....eeeeeeeeeeeee....hhhhhhhhhhhhh........eeeeeeeee............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hrd A   2 GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARIVSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDAIAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIHQVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGMLTVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHCALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVEMFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFRGFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENSVGLIETLEKAREKAVEVMGY 421
                                    11        21        31        41        51        61        71        81        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


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with NDMMS_EUBBA | Q0QLF1 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
          NDMMS_EUBBA     1 MKKRGKGVGSMWYGIGNTGLPNPAAAFVEIHGDGSANVMFGAADIGQGSGTAMAQIAAEELGLDYEKIHVTWGDTMVTPDGGATSASRQTLITGNAVILACRQAKETLAKTAAEKLDCAPEELSFRDNTVFITADPERSMTYGELMAAMKAAGRMAVGAGSYNPNTTGLAPENMSGIPFEVYSYATTIAEVEVDTETGEVDVLKVVSAHDVGTPINRSMVEGQIEGGVTMGQGFVLMEEIEVNTKNGAIKNPSMSKYIIPSNRDVPEIHSILVESEGGPGPFGAKGVGEPALIPMIPAVVAAIEDALGTRFTHTPIMPKDIVAAVKAQEK 330
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.........eeeeeee.....eeeee.......hhhhhhhhhhhhhhh.hhh.eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhh...eeeeeee...................eeeeeeeeeeeee.....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.............................eeeeeeee.....hhhhh.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hrd B   1 MKKRGKGVGSMWYGIGNTGLPNPAAAFVEIHGDGSANVMFGAADIGQGSGTAMAQIAAEELGLDYEKIHVTWGDTMVTPDGGATSASRQTLITGNAVILACRQAKETLAKTAAEKLDCAPEELSFRDNTVFITADPERSMTYGELMAAMKAAGRMAVGAGSYNPNTTGLAPENMSGIPFEVYSYATTIAEVEVDTETGEVDVLKVVSAHDVGTPINRSMVEGQIEGGVTMGQGFVLMEEIEVNTKNGAIKNPSMSKYIIPSNRDVPEIHSILVESEGGPGPFGAKGVGEPALIPMIPAVVAAIEDALGTRFTHTPIMPKDIVAAVKAQEK 330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with NDFS_EUBBA | Q0QLF4 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           NDFS_EUBBA     1 MKDFEFFAPKTLEEAKGLLHQYKDVPPAIIAGGTDLVIEINDRWEKPDVVIDIKKLKELEYIRVEENTIHIGALSTFTQIENHPFIRSHVRALYKAASQVGSPQIRNLGTIGGNLSTSSVAGDGVSAMTTLDATVVLESVRGTRQMKLTDFFDGEGFKRRNALEADEIMTEVIIDRPDAHSASAFYKLAKRKSLAISVIGGGMAVKVDDAGVCTWASMRGGCIGRYPLHFKQAEEMLVGAPLTMETMEATLPILHDTVYDMARARPSVLYKKESVQGVFKKLFVDILDQLE 291
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhhhhh.....eee....hhhhhhhh......eeee...hhhhh.eee...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeee..eeeeeehhhhhhh.............eeeeeeee.....eeeeeeee..........eeeeeeeeee...eeeeeeeeee......eehhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FAD_PCMH  PDB: C:1-179 UniProt: 1-179                                                                                                                                              ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrd C   1 MKDFEFFAPKTLEEAKGLLHQYKDVPPAIIAGGTDLVIEINDRWEKPDVVIDIKKLKELEYIRVEENTIHIGALSTFTQIENHPFIRSHVRALYKAASQVGSPQIRNLGTIGGNLSTSSVAGDGVSAMTTLDATVVLESVRGTRQMKLTDFFDGEGFKRRNALEADEIMTEVIIDRPDAHSASAFYKLAKRKSLAISVIGGGMAVKVDDAGVCTWASMRGGCIGRYPLHFKQAEEMLVGAPLTMETMEATLPILHDTVYDMARARPSVLYKKESVQGVFKKLFVDILDQLE 291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 


Chain D from PDB  Type:PROTEIN  Length:160
 aligned with NDSFS_EUBBA | Q0QLF3 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:160
                                                                                                                                                                                      157   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -
          NDSFS_EUBBA     1 MNKITINLNLNGEARSIVTEPNKRLLDLLREDFGLTSVKEGCSEGECGACTVIFNGDPVTTCCMLAGQADESTIITLEGVAEDGKPSLLQQCFLEAGAVQCGYCTPGMILTAKALLDKNPDPTDEEITVAMSGNLCRCTGYIKIHAAVRYAVERCAN---   -
               SCOP domains d3hrdd1 D:1-82 automated matches                                                  d3hrdd2 D:83-160 automated matches                                             SCOP domains
               CATH domains 3hrdD01 D:1-79  [code=3.10.20.30, no name defined]                             3hrdD02 D:80-160  [code=1.10.150.120, no name defined]                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeee....hhhhhhhh...................eeee..eeee.hhhhhhhhh.eeeehhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---2FE2S_FER_2  PDB: D:4-80 UniProt: 4-80                                       -------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------2FE2S_FER-------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrd D   1 MNKITINLNLNGEARSIVTEPNKRLLDLLREDFGLTSVKEGCSEGECGACTVIFNGDPVTTCCMLAGQADESTIITLEGVAEDGKPSLLQQCFLEAGAVQCGYCTPGMILTAKALLDKNPDPTDEEITVAMSGNLCRCTGYIKIHAAVRYAVERCANAAA 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain E from PDB  Type:PROTEIN  Length:420
 aligned with NDLMS_EUBBA | Q0QLF2 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:420
                                    11        21        31        41        51        61        71        81        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
          NDLMS_EUBBA     2 GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARIVSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDAIAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIHQVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGMLTVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHCALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVEMFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFRGFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENSVGLIETLEKAREKAVEVMGY 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhh....hhhhh.....eeeeeee.......eeeeehhhhhh...eeeeehhhhh..........................eeeeeee.hhhhhhhhhhh.eeee.......hhhhhhh...........eeeeeeeee.hhhhhh....eeeeeeeee...........eeeeee.....eeeee...hhhhhhhhhhhhhh.hhh.eeeee..............hhhhhhhhhhhhh..eeee.hhhhhhhhh.....eeeeeeeee.....eeeeeeeeeeeee....hhhhhhhhhhhhh........eeeeeeeee............hhhhhhhhhhhhhhhhhhh.....hhhhhhhh.................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hrd E   2 GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARIVSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDAIAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIHQVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGMLTVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHCALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVEMFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFRGFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENSVGLIETLEKAREKAVEVMGY 421
                                    11        21        31        41        51        61        71        81        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


Chain F from PDB  Type:PROTEIN  Length:330
 aligned with NDMMS_EUBBA | Q0QLF1 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
          NDMMS_EUBBA     1 MKKRGKGVGSMWYGIGNTGLPNPAAAFVEIHGDGSANVMFGAADIGQGSGTAMAQIAAEELGLDYEKIHVTWGDTMVTPDGGATSASRQTLITGNAVILACRQAKETLAKTAAEKLDCAPEELSFRDNTVFITADPERSMTYGELMAAMKAAGRMAVGAGSYNPNTTGLAPENMSGIPFEVYSYATTIAEVEVDTETGEVDVLKVVSAHDVGTPINRSMVEGQIEGGVTMGQGFVLMEEIEVNTKNGAIKNPSMSKYIIPSNRDVPEIHSILVESEGGPGPFGAKGVGEPALIPMIPAVVAAIEDALGTRFTHTPIMPKDIVAAVKAQEK 330
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.........eeeeeee.....eeeee.......hhhhhhhhhhhhhhh.hhh.eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhh...eeeeeee...................eeeeeeeeeeeee.....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.............................eeeeeee......hhhhh.........hhhhhhhhhhhhhhh........hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hrd F   1 MKKRGKGVGSMWYGIGNTGLPNPAAAFVEIHGDGSANVMFGAADIGQGSGTAMAQIAAEELGLDYEKIHVTWGDTMVTPDGGATSASRQTLITGNAVILACRQAKETLAKTAAEKLDCAPEELSFRDNTVFITADPERSMTYGELMAAMKAAGRMAVGAGSYNPNTTGLAPENMSGIPFEVYSYATTIAEVEVDTETGEVDVLKVVSAHDVGTPINRSMVEGQIEGGVTMGQGFVLMEEIEVNTKNGAIKNPSMSKYIIPSNRDVPEIHSILVESEGGPGPFGAKGVGEPALIPMIPAVVAAIEDALGTRFTHTPIMPKDIVAAVKAQEK 330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330


Chain G from PDB  Type:PROTEIN  Length:292
 aligned with NDFS_EUBBA | Q0QLF4 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  
           NDFS_EUBBA     1 MKDFEFFAPKTLEEAKGLLHQYKDVPPAIIAGGTDLVIEINDRWEKPDVVIDIKKLKELEYIRVEENTIHIGALSTFTQIENHPFIRSHVRALYKAASQVGSPQIRNLGTIGGNLSTSSVAGDGVSAMTTLDATVVLESVRGTRQMKLTDFFDGEGFKRRNALEADEIMTEVIIDRPDAHSASAFYKLAKRKSLAISVIGGGMAVKVDDAGVCTWASMRGGCIGRYPLHFKQAEEMLVGAPLTMETMEATLPILHDTVYDMARARPSVLYKKESVQGVFKKLFVDILDQLEG 292
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhhhhh.....eee....hhhhhhhh......eeee...hhhhh.eee...eeeee...hhhhhhhh......hhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeee........hhhhhhhh.............eeeeeeee.....eeeeeeee..........eeeeeeeee.....eeeeeeee.......eehhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FAD_PCMH  PDB: G:1-179 UniProt: 1-179                                                                                                                                              ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrd G   1 MKDFEFFAPKTLEEAKGLLHQYKDVPPAIIAGGTDLVIEINDRWEKPDVVIDIKKLKELEYIRVEENTIHIGALSTFTQIENHPFIRSHVRALYKAASQVGSPQIRNLGTIGGNLSTSSVAGDGVSAMTTLDATVVLESVRGTRQMKLTDFFDGEGFKRRNALEADEIMTEVIIDRPDAHSASAFYKLAKRKSLAISVIGGGMAVKVDDAGVCTWASMRGGCIGRYPLHFKQAEEMLVGAPLTMETMEATLPILHDTVYDMARARPSVLYKKESVQGVFKKLFVDILDQLEG 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  


Chain H from PDB  Type:PROTEIN  Length:157
 aligned with NDSFS_EUBBA | Q0QLF3 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          NDSFS_EUBBA     1 MNKITINLNLNGEARSIVTEPNKRLLDLLREDFGLTSVKEGCSEGECGACTVIFNGDPVTTCCMLAGQADESTIITLEGVAEDGKPSLLQQCFLEAGAVQCGYCTPGMILTAKALLDKNPDPTDEEITVAMSGNLCRCTGYIKIHAAVRYAVERCAN 157
               SCOP domains d3hrdh1 H:1-82 automated matches                                                  d3hrdh2 H:83-157 automated matches                                          SCOP domains
               CATH domains 3hrdH01 H:1-79  [code=3.10.20.30, no name defined]                             3hrdH02 H:80-157  [code=1.10.150.120, no name defined]                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeee....hhhhhhhhh..................eeee..eeee.hhhhhhhhh.eeeehhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhhhh........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---2FE2S_FER_2  PDB: H:4-80 UniProt: 4-80                                       ----------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------2FE2S_FER----------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hrd H   1 MNKITINLNLNGEARSIVTEPNKRLLDLLREDFGLTSVKEGCSEGECGACTVIFNGDPVTTCCMLAGQADESTIITLEGVAEDGKPSLLQQCFLEAGAVQCGYCTPGMILTAKALLDKNPDPTDEEITVAMSGNLCRCTGYIKIHAAVRYAVERCAN 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HRD)

(-) Gene Ontology  (12, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,E   (NDLMS_EUBBA | Q0QLF2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050138    nicotinate dehydrogenase activity    Catalysis of the reaction: H(2)O + NADP(+) + nicotinate = 6-hydroxynicotinate + H(+) + NADPH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0051187    cofactor catabolic process    The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain B,F   (NDMMS_EUBBA | Q0QLF1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050138    nicotinate dehydrogenase activity    Catalysis of the reaction: H(2)O + NADP(+) + nicotinate = 6-hydroxynicotinate + H(+) + NADPH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0051187    cofactor catabolic process    The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain C,G   (NDFS_EUBBA | Q0QLF4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0050138    nicotinate dehydrogenase activity    Catalysis of the reaction: H(2)O + NADP(+) + nicotinate = 6-hydroxynicotinate + H(+) + NADPH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0051187    cofactor catabolic process    The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain D,H   (NDSFS_EUBBA | Q0QLF3)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050138    nicotinate dehydrogenase activity    Catalysis of the reaction: H(2)O + NADP(+) + nicotinate = 6-hydroxynicotinate + H(+) + NADPH.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0051187    cofactor catabolic process    The chemical reactions and pathways resulting in the breakdown of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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