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Enzyme   1.12.98.1
Classification oxidoreductase    | release date: Wed, Dec 12, 2012
Title cryo-em structure of the f420-reducing nife-hydrogenase from a methanogenic archaeon with bound substrate
Authors D.J.MILLS, J.VONCK, M.STRAUSS, S.SHIMA, S.VITT
Method ELECTRON MICROSCOPY (resolution: 4.00Å)
PDBe Citation   
Small molecules:    search SF4 SF4 binding statistics SF4   search NI NI binding statistics NI   search FE2 FE2 binding statistics FE2   search F42 F42 binding statistics F42   search FAD FAD binding statistics FAD   search FCO FCO binding statistics FCO
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
MSERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAPETAPVMVQRICGVCPIPHTLASVEAIDD
SLDIEVPKAGRLLRELTLAAHHVNSHAIHHFLIAPDFVPENLMADAINSVSEIRKNAQYVVDMVAGEGIHPSDVRIGGMA
DNITELARKRLYARLKQLKPKVNEHVELMIGLIEDKGLPEGLGVHNQPTLASHQIYGDRTKFDLDRFTEIMPESWYDDPE
IAKRACSTIPLYDGRNVEVGPRARMVEFQGFKERGVVAQHVARALEMKTALSRAIEILDELDTSAPVRADFDERGTGKLG
IGAIEAPRGLDVHMAKVENGKIQFYSALVPTTWNIPTMGPATEGFHHEYGPHVIRAYDPCLSCATHVMVVDDEDKSVIKN
EMVKI
Chain B sequence:
MSLIARIKRFLGLEAEAKREEPEKEKSEPVGASKEEVEKVAEENAKPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVD
IVYGQTLVDLWEMPEMDLALVEGSVCLQDEHSLHELKELREKAKLVCAFGSCAATGCFTRYSRGGQQAQPSHESFVPIAD
LIDVDLALPGCPPSPEIIAKTVVALLNNDMDYLQPMLDLAGYTEACGCDLQTKVVNQGLCIGCGTCAMACQTRALDMTNG
RPELNSDRCIKCGICYVQCPRSWWPEEQIKKELGL
Chain C sequence:
MVLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWKPQPMVAMSSDELKAAAGTKYTFSP
NVMMLKKAVRQYGIEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFICEKLGVSMELVEK
MDIGKGKFWVYTQDDVLTLPLKETHGYEQAGCKICKDYVAELADVSTGSVGSPDGWSTVITRTDAGDSIFKQAVEAGLFE
TKPIEEVKPGLGLLEKLAAQKKEKAEKNIAARKEMGLPTPF
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : F420-REDUCING HYDROGENASE, SUBUNIT ALPHA
member of: GENE3D:searchG3DSA_1.10.645.10PANTHER:searchPTHR11993/searchPTHR11993_SF9PFAM:searchPF00374PROSITE PATTERNS:searchPS00507/searchPS00508, SUPERFAMILY:searchSSF56762TIGRFAMS:searchTIGR03295UniProt:searchD9PYF9
JMol viewer RasMol script viewer  FE2 2991A  ..                                                                                                                                                                                                                                                                                                                                                                                                 
JMol viewer RasMol script viewer  NI 2990A  ..                                                                                                                                                                                                                                                                                                                                                                                                 
JMol viewer RasMol script viewer  FCO 2989A  ..                                                                                                                                                                                                                                                                                                                                                                                                 
sec str:  ....eeeeee......eeeeeee......eeeeeee.......hhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............................................hhhhhh................hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.................eeeeeee......eeeeee.......eeeeeehhhhh...hhhhh.........hhhhh....hhhhh.
sequence :  ..SERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAPETAPVMVQRICGVCPIPHTLASVEAIDDSLDIEVPKAGRLLRELTLAAHHVNSHAIHHFLIAPDFVPENLMADAINSVSEIRKNAQYVVDMVAGEGIHPSDVRIGGMADNITELARKRLYARLKQLKPKVNEHVELMIGLIEDKGLPEGLGVHNQPTLASHQIYGDRTKFDLDRFTEIMPESWYDDPEIAKRACSTIPLYDGRNVEVGPRARMVEFQGFKERGVVAQHVARALEMKTALSRAIEILDELDTSAPVRADFDERGTGKLGIGAIEAPRGLDVHMAKVENGKIQFYSALVPTTWNIPTMGPATEGFHHEYGPHVIRAYDPCLSCATH
seq num:  ..2         12        22        32        42        52        62        72        82        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  
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..| |     ||| |                          |      | |            |  |                                                              |  |               |    |    |   ^***                               |    |                 |  |          |  |                                                                              | |                                                          |  |  |  |
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..^**     ^** |                          |      ^**            |  |                                                              |  |               |    |    |    |                                 |    |                 |  |          |  |                                                                              ^**                                                          |  |  |  |
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..         ^***                          |                     |  |                                                              ^***               |    |    |    |                                 |    |                 ^***          ^***                                                                                                                                           |  |  |  |
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..                                       |                     |  |                                                                                 ^*****    ^*****                                 ^*****                                                                                                                                                                              |  |  |  |
search RasMol script viewer Motif-ligand binding stats  NI_HGENASE_L_1 ..                                       **********************^**^                                                                                                                                                                                                                                                                                                                      |  |  |  |
search RasMol script viewer Motif-ligand binding stats  NI_HGENASE_L_2 ..                                                                                                                                                                                                                                                                                                                                                                                       ***^**^***

chain B : F420-REDUCING HYDROGENASE, SUBUNIT GAMMA
member of: GENE3D:searchG3DSA_3.30.70.20/searchG3DSA_3.40.50.700PANTHER:searchPTHR11995/searchPTHR11995_SF6PFAM:searchPF01058/searchPF13237PROSITE PATTERNS:searchPS00198, PROSITE PROFILES:searchPS51379, SUPERFAMILY:searchSSF56770TIGRFAMS:searchTIGR03294UniProt:searchD9PYF7
JMol viewer RasMol script viewer  SF4 302B  ..                                                                                                                                              ..                     ******                                              
JMol viewer RasMol script viewer  SF4 301B  ..                                                                                                                                              ..                     ||||||                      * *** *                 
JMol viewer RasMol script viewer  SF4 300B  ..          ** *                                                                      ***                                                       ..                     ||||||                      | ||| |                 
sec str:  ....eeeee......hhhhhhh........hhhhh.eeee.............eeeeee........hhhhhhhhhhh....eeeee...................................eeee.....hhhhhhhhhhhh............................hhhhh.....eeee...eee.....................hhhhhhh
sequence :  ..KPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVDIVYGQTLVDLWEMPEMDLALVEGSVCLQDEHSLHELKELREKAKLVCAFGSCAATGCFTRYSRGGQQAQPSHESFVPIADLIDVDLALPGCPPSPEIIAKTVVALLN..AGYTEACGCDLQTKVVNQGLCIGCGTCAMACQTRALDMTNGRPELNSDRCIKCGICYVQCPRSWWPEEQIKKE
seq num:  ..46        56        66        76        86        96        106       116       126       136       146       156       166       176         ..200       210       220       230       240       250       260          
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..                 |  |                   |  |                      |  |              |    |        |    |                                      ..                  |    |                      ^**|  |  |   ||            
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..                 ^***                   ^***                      ^***              |    |        |    |                                      ..                  |    |                         |  |  |   ||            
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..                                                                                    ^*****        ^*****                                      ..                  ^*****                         |  |  |   ||            
search RasMol script viewer Motif-ligand binding stats  4FE4S_FER_1 ..                                                                                                                                              ..                                                 ^**^**^***^*            

chain C : F420-REDUCING HYDROGENASE, SUBUNIT BETA
member of: PANTHER:searchPTHR31332/searchPTHR31332_SF0PFAM:searchPF04422/searchPF04432TIGRFAMS:searchTIGR03289UniProt:searchD9PYF6
JMol viewer RasMol script viewer  FAD 304C  ..                     *** **                 **                       * * *                                                       *                                                                           **                                                                       
JMol viewer RasMol script viewer  SF4 303C  ..                     ||| ||                 ||                       | | |                          **                           | *                                                                         ||                                                                       
JMol viewer RasMol script viewer  F42 285C  ..                     ||| ||                 ||                       | | |                          ||                           | |                             *                                           |**      *                                                               
sec str:  .......eeeeee...hhhh......hhhhhhhhhhhh....eeeeeee.......eeeeee.hhhhhhhh...........hhhhhhhhh....eeeeeee...hhhhhhhhh.............eeeee.......hhhhhhhhhh.....hhh.eeeeee..eeeee....eeeeeehhhhh..................eeeee.......eeeee..hhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhh......
sequence :  ..LGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWKPQPMVAMSSDELKAAAGTKYTFSPNVMMLKKAVRQYGIEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFICEKLGVSMELVEKMDIGKGKFWVYTQDDVLTLPLKETHGYEQAGCKICKDYVAELADVSTGSVGSPDGWSTVITRTDAGDSIFKQAVEAGLFETKPIEEVKPGLGLLEKLAAQKKEKAEKNIAARKEMGLPTP
seq num:  ..3         13        23        33        43        53        63        73        83        93        103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273     
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..  ^**|  ^** ^**|       |    |        |    |                  |  |     |    |                                                                                             |  |               |    |              |    |    |  |            |    |                                      
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..  ^***      ^***       |    |        |    |                  ^***     |    |                                                                                             ^***               |    |              |    |    ^***            |    |                                      
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..                       ^*****        ^*****                           ^*****                                                                                                                ^*****              ^*****                    ^*****                                      

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