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

(-) Description

Title :  NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, DITHIONITE-REDUCED STATE
 
Authors :  S. M. Mayer, D. M. Lawson, C. A. Gormal, S. M. Roe, B. E. Smith
Date :  06 May 99  (Deposition) - 01 Nov 99  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Biological Nitrogen Fixation, Nitrogen Metabolism, Molybdoenzymes, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Mayer, D. M. Lawson, C. A. Gormal, S. M. Roe, B. E. Smith
New Insights Into Structure-Function Relationships In Nitrogenase: A 1. 6 A Resolution X-Ray Crystallographic Study Of Klebsiella Pneumoniae Mofe-Protein.
J. Mol. Biol. V. 292 871 1999
PubMed-ID: 10525412  |  Reference-DOI: 10.1006/JMBI.1999.3107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)
    Cellular Location: CYTOPLASM
    Chains: A, C
    EC Number: 1.18.6.1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Other Details: CHAINS A AND C ARE ALPHA-SUBUNITS
    Other Details - Source: ALSO KNOWN AS KLEBSIELLA PNEUMONIAE OXYTOCA
    Strain: M5A1
    Synonym: NITROGENASE COMPONENT 1
    Variant: WILD-TYPE
 
Molecule 2 - PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)
    Cellular Location: CYTOPLASM
    Chains: B, D
    EC Number: 1.18.6.1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Other Details: CHAINS B AND D ARE BETA-SUBUNITS
    Other Details - Source: ALSO KNOWN AS KLEBSIELLA PNEUMONIAE OXYTOCA
    Strain: M5A1
    Synonym: NITROGENASE COMPONENT 1
    Variant: WILD-TYPE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 31)

Asymmetric/Biological Unit (6, 31)
No.NameCountTypeFull Name
1CFM2Ligand/IonFE-MO-S CLUSTER
2CL2Ligand/IonCHLORIDE ION
3CLF2Ligand/IonFE(8)-S(7) CLUSTER
4EDO16Ligand/Ion1,2-ETHANEDIOL
5HCA2Ligand/Ion3-HYDROXY-3-CARBOXY-ADIPIC ACID
6MG7Ligand/IonMAGNESIUM ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN D:395 , HOH D:3089BINDING SITE FOR RESIDUE CL D 2771
02AC2SOFTWAREASN B:395 , TRP B:398 , HOH B:3112BINDING SITE FOR RESIDUE CL B 2772
03AC3SOFTWAREHOH A:3605 , HOH A:3606 , HOH A:3607 , HOH B:3783 , HOH B:3784 , HOH B:3785BINDING SITE FOR RESIDUE MG A 3001
04AC4SOFTWAREASP B:349 , ASP B:353 , HOH B:3786 , LYS D:106 , GLU D:107 , HOH D:3796BINDING SITE FOR RESIDUE MG B 3002
05AC5SOFTWAREHOH B:3787 , HOH B:3788 , HOH B:3789 , HOH B:3790 , HOH B:3791 , HOH B:3792BINDING SITE FOR RESIDUE MG B 3003
06AC6SOFTWAREASP B:407 , HOH B:3793 , HOH B:3794 , HOH B:3795 , HOH B:3796 , HOH B:3797BINDING SITE FOR RESIDUE MG B 3004
07AC7SOFTWAREHOH C:3027 , HOH C:3028 , HOH C:3029 , HOH C:3031 , HOH D:3797 , HOH D:3798BINDING SITE FOR RESIDUE MG C 3005
08AC8SOFTWARELYS B:106 , GLU B:107 , HOH B:3798 , ASP D:349 , ASP D:353 , HOH D:3799BINDING SITE FOR RESIDUE MG D 3006
09AC9SOFTWAREHOH D:3800 , HOH D:3801 , HOH D:3802 , HOH D:3803 , HOH D:3804 , HOH D:3805BINDING SITE FOR RESIDUE MG D 3007
10BC1SOFTWAREALA A:64 , ARG A:95 , GLN A:190 , GLY A:422 , ILE A:423 , HIS A:440 , CFM A:503 , HOH A:3007 , HOH A:3008 , HOH A:3009 , HOH A:3026 , HOH A:3032 , HOH A:3043 , HOH A:3592 , HOH A:3593 , HOH A:3594 , HOH B:3017BINDING SITE FOR RESIDUE HCA A 501
11BC2SOFTWAREVAL A:69 , ARG A:95 , HIS A:194 , TYR A:227 , CYS A:273 , GLY A:354 , GLY A:355 , LEU A:356 , ARG A:357 , PHE A:379 , HIS A:440 , HCA A:501BINDING SITE FOR RESIDUE CFM A 503
12BC3SOFTWARECYS A:61 , TYR A:63 , PRO A:84 , GLY A:86 , CYS A:87 , TYR A:90 , CYS A:153 , GLY A:184 , CYS B:68 , SER B:90 , CYS B:93 , TYR B:96 , CYS B:151 , SER B:186BINDING SITE FOR RESIDUE CLF A 505
13BC4SOFTWAREALA C:64 , ARG C:95 , GLN C:190 , GLY C:422 , ILE C:423 , HIS C:440 , CFM C:503 , HOH C:1382 , HOH C:1391 , HOH C:1392 , HOH C:1393 , HOH C:1396 , HOH C:1963 , HOH C:1966 , HOH C:2004 , HOH C:2031 , HOH D:3041BINDING SITE FOR RESIDUE HCA C 501
14BC5SOFTWAREVAL C:69 , ARG C:95 , HIS C:194 , TYR C:227 , CYS C:273 , GLY C:354 , GLY C:355 , LEU C:356 , ARG C:357 , PHE C:379 , HIS C:440 , HCA C:501BINDING SITE FOR RESIDUE CFM C 503
15BC6SOFTWARECYS C:61 , TYR C:63 , PRO C:84 , GLY C:86 , CYS C:87 , TYR C:90 , CYS C:153 , GLY C:184 , CYS D:68 , SER D:90 , CYS D:93 , TYR D:96 , CYS D:151 , SER D:186BINDING SITE FOR RESIDUE CLF C 505
16BC7SOFTWAREASP A:443 , THR D:356 , TRP D:357 , HOH D:3008 , HOH D:3150BINDING SITE FOR RESIDUE EDO D 2773
17BC8SOFTWARELYS A:75 , THR A:100 , ASP A:254 , HOH A:3600 , PHE B:23 , GLU B:30 , HOH B:3784BINDING SITE FOR RESIDUE EDO A 2774
18BC9SOFTWAREALA A:93 , ARG A:95 , ASN A:97 , TYR A:98 , THR A:110 , HOH A:3134 , HOH D:3070BINDING SITE FOR RESIDUE EDO A 2775
19CC1SOFTWAREARG A:209 , GLU A:261 , HOH A:3191 , GLN D:36 , HOH D:3445BINDING SITE FOR RESIDUE EDO A 2776
20CC2SOFTWARELYS A:267 , GLN A:313 , PHE A:314 , HOH A:3196 , HOH A:3231 , HOH A:3346 , HOH A:3548BINDING SITE FOR RESIDUE EDO A 2777
21CC3SOFTWARETHR B:356 , TRP B:357 , HOH B:3764 , HOH B:3765 , ASP C:443BINDING SITE FOR RESIDUE EDO B 2778
22CC4SOFTWAREPRO C:176 , ASN C:208 , ARG C:209 , GLU C:261 , HOH C:1542 , HOH C:1544BINDING SITE FOR RESIDUE EDO C 2779
23CC5SOFTWAREASN A:48 , LEU A:192 , HIS A:195 , HOH A:3089 , HOH A:3186 , HOH A:3527BINDING SITE FOR RESIDUE EDO A 2780
24CC6SOFTWARELYS B:237 , SER B:248 , LEU B:249 , ASP B:252 , GLU B:276 , HOH B:3471 , HOH B:3751BINDING SITE FOR RESIDUE EDO B 2781
25CC7SOFTWAREGLU B:51 , PHE B:55 , ARG B:433 , HOH B:3538 , HOH B:3559 , HOH B:3580BINDING SITE FOR RESIDUE EDO B 2782
26CC8SOFTWAREASN B:54 , PHE B:55 , ARG B:57 , CYS B:421 , HIS B:425 , HOH B:3741BINDING SITE FOR RESIDUE EDO B 2783
27CC9SOFTWAREHIS B:474 , ARG B:477 , MET D:350 , THR D:491 , HOH D:3013 , HOH D:3015 , HOH D:3269BINDING SITE FOR RESIDUE EDO D 2784
28DC1SOFTWARELYS D:237 , SER D:248 , LEU D:249 , ASP D:252 , GLU D:276 , HOH D:3392BINDING SITE FOR RESIDUE EDO D 2785
29DC2SOFTWARETYR A:444 , TYR B:11 , LEU D:501 , SER D:514 , ARG D:519 , HOH D:3010BINDING SITE FOR RESIDUE EDO D 2786
30DC3SOFTWAREASN D:54 , PHE D:55 , ARG D:57 , HIS D:425 , HOH D:3664BINDING SITE FOR RESIDUE EDO D 2787
31DC4SOFTWARELYS A:171 , HOH A:3433 , ARG D:27 , GLN D:28 , GLU D:30 , GLU D:31 , ALA D:32BINDING SITE FOR RESIDUE EDO D 2788

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Trp A:251 -Ser A:252
2Gly A:446 -Pro A:447
3Tyr B:11 -Pro B:12
4Phe B:467 -Pro B:468
5Trp C:251 -Ser C:252
6Gly C:446 -Pro C:447
7Tyr D:11 -Pro D:12
8Phe D:467 -Pro D:468

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NITROGENASE_1_1PS00699 Nitrogenases component 1 alpha and beta subunits signature 1.NIFD_KLEPN82-89
 		  2A:80-87
C:80-87
NIFK_KLEPN87-94
 		  2B:86-93
D:86-93
2NITROGENASE_1_2PS00090 Nitrogenases component 1 alpha and beta subunits signature 2.NIFK_KLEPN150-164
 		  2B:149-163
D:149-163
NIFD_KLEPN153-167
 		  2A:151-165
C:151-165

(-) Exons   (0, 0)

(no "Exon" information available for 1QGU)

(-) 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:478
 aligned with NIFD_KLEPN | P00466 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:478
                                    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       392       402       412       422       432       442       452       462       472        
           NIFD_KLEPN     3 TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPAGCGQYSRAERRNYYTGVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDGFAIFARDMDMTLNNPAWNELTAPWL 480
               SCOP domains d1qgua_ A: Nitrogenase iron-molybdenum protein, alpha chain                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qguA01 A:1-61,A:343-477                                     1qguA02 A:62-204 Nitrogenase molybdenum iron protein domain                                                                                    1qguA03 A:205-318 Nitrogenase molybdenum iron protein domain                                                      ------------------------1qguA01 A:1-61,A:343-477 Nitrogenase molybdenum iron protein domain                                                                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhheee........hhh.................hhhhh..........eeeeee...hhhhh............................hhhhhh..hhhhhhhhhhhhhh.....eeeeee..hhhhh...hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh...............eeeee....hhhhhhhhhhhhhh...eeeeee.....hhhhh.hhh..eeee..hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhh.hhhhhhh..eeeeeee....hhhhhhhhhh.....eeee...hhhhhhhhhhh...eeee.hhhhhhhhh...eeee...hhh.....hhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------NITROGEN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qgu A   1 TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPVGCGQYSRAGRRNYYTGVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDGFAIFARDMDMTLNNPAWNELTAPWL 478
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470        


Chain B from PDB  Type:PROTEIN  Length:519
 aligned with NIFK_KLEPN | P09772 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:519
                                    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       431       441       451       461       471       481       491       501       511         
           NIFK_KLEPN     2 SQTIDKINSCYPLFEQDEYQELFRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR 520
               SCOP domains d1qgub_ B: Nitrogenase iron-molybdenum protein, beta chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------1qguB01 B:68-211 Nitrogenase molybdenum iron protein domain                                                                                     1qguB02 B:212-316 Nitrogenase molybdenum iron protein domain                                             1qguB04 B:317-360,B:481-519                 1qguB03 B:361-466 Nitrogenase molybdenum iron protein domain                                              --------------1qguB04 B:317-360,B:481-519             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhh............hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.....eee....hhhhhh..hhhhhhhhhhhhhhh...eeeeee.hhhhhh...hhhhhhhhhh.....................hhhhhhhhhhhhhhhhh...........eeeee......hhhhhhhhhhhhhh..eeee........................hhhhh.hhh..eeee......hhhhhhhhh..............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh.......eeee...hhhhhhhhhhh...eeee.hhhhhhhhhhhhh.hhh..eeee..........hhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------NITROGEN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qgu B   1 SQTIDKINSCYPLFEQDEYQELFRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR 519
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510         


Chain C from PDB  Type:PROTEIN  Length:478
 aligned with NIFD_KLEPN | P00466 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:478
                                    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       392       402       412       422       432       442       452       462       472        
           NIFD_KLEPN     3 TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPAGCGQYSRAERRNYYTGVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDGFAIFARDMDMTLNNPAWNELTAPWL 480
               SCOP domains d1qguc_ C: Nitrogenase iron-molybdenum protein, alpha chain                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qguC01 C:1-61,C:343-477                                     1qguC02 C:62-204 Nitrogenase molybdenum iron protein domain                                                                                    1qguC03 C:205-318 Nitrogenase molybdenum iron protein domain                                                      ------------------------1qguC01 C:1-61,C:343-477 Nitrogenase molybdenum iron protein domain                                                                    - CATH domains
           Pfam domains (1) ------------------------------------------------------------Oxidored_nitro-1qguC01 C:61-466                                                                                                                                                                                                                                                                                                                                                                                       ------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------Oxidored_nitro-1qguC02 C:61-466                                                                                                                                                                                                                                                                                                                                                                                       ------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhhheee............................hhhhh..........eeeeee...hhhhh............................hhhhhh..hhhhhhhhhhhhhh.....eeeeee..hhhh....hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh...............eeeee....hhhhhhhhhhhhhh...eeeeee.....hhhhh.hhh..eeee..hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhh.hhhhhhh..eeeeeee....hhhhhhhhhh.....eeee...hhhhhhhhhhh...eeee.hhhhhhhhh....eee...hhh.....hhhhhhhhhhhhhhhh..hhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------NITROGEN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qgu C   1 TNATGERNLALIQEVLEVFPETARKERRKHMMVSDPKMKSVGKCIISNRKSQPGVMTVRGCAYAGSKGVVFGPIKDMAHISHGPVGCGQYSRAGRRNYYTGVSGVDSFGTLNFTSDFQERDIVFGGDKKLSKLIEEMELLFPLTKGITIQSECPVGLIGDDISAVANASSKALDKPVIPVRCEGFRGVSQSLGHHIANDVVRDWILNNREGQPFETTPYDVAIIGDYNIGGDAWASRILLEEMGLRVVAQWSGDGTLVEMENTPFVKLNLVHCYRSMNYIARHMEEKHQIPWMEYNFFGPTKIAESLRKIADQFDDTIRANAEAVIARYEGQMAAIIAKYRPRLEGRKVLLYMGGLRPRHVIGAYEDLGMEIIAAGYEFAHNDDYDRTLPDLKEGTLLFDDASSYELEAFVKALKPDLIGSGIKEKYIFQKMGVPFRQMHSWDYSGPYHGYDGFAIFARDMDMTLNNPAWNELTAPWL 478
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470        


Chain D from PDB  Type:PROTEIN  Length:519
 aligned with NIFK_KLEPN | P09772 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:519
                                    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       431       441       451       461       471       481       491       501       511         
           NIFK_KLEPN     2 SQTIDKINSCYPLFEQDEYQELFRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR 520
               SCOP domains d1qgud_ D: Nitrogenase iron-molybdenum protein, beta chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------1qguD01 D:68-211 Nitrogenase molybdenum iron protein domain                                                                                     1qguD02 D:212-316 Nitrogenase molybdenum iron protein domain                                             1qguD04 D:317-360,D:481-519                 1qguD03 D:361-466 Nitrogenase molybdenum iron protein domain                                              --------------1qguD04 D:317-360,D:481-519             CATH domains
           Pfam domains (1) DUF3364-1qguD01 D:1-54                                -------------Oxidored_nitro-1qguD03 D:68-498                                                                                                                                                                                                                                                                                                                                                                                                                --------------------- Pfam domains (1)
           Pfam domains (2) DUF3364-1qguD02 D:1-54                                -------------Oxidored_nitro-1qguD04 D:68-498                                                                                                                                                                                                                                                                                                                                                                                                                --------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhh............hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.....eee....hhhhhh..hhhhhhhhhhhhhhh...eeeeee.hhhhhh...hhhhhhhhhh.....................hhhhhhhhhhhhhhhhh...........eeeee......hhhhhhhhhhhhh...eeee........................hhhhh.hhh..eeee......hhhhhhhhh..............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh..hhh...eeee...hhhhhhhhhh....eeee.hhhhhhhhhhhhh.hhh..eeee..........hhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------NITROGEN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qgu D   1 SQTIDKINSCYPLFEQDEYQELFRNKRQLEEAHDAQRVQEVFAWTTTAEYEALNFRREALTVDPAKACQPLGAVLCSLGFANTLPYVHGSQGCVAYFRTYFNRHFKEPIACVSDSMTEDAAVFGGNNNMNLGLQNASALYKPEIIAVSTTCMAEVIGDDLQAFIANAKKDGFVDSSIAVPHAHTPSFIGSHVTGWDNMFEGFAKTFTADYQGQPGKLPKLNLVTGFETYLGNFRVLKRMMEQMAVPCSLLSDPSEVLDTPADGHYRMYSGGTTQQEMKEAPDAIDTLLLQPWQLLKSKKVVQEMWNQPATEVAIPLGLAATDELLMTVSQLSGKPIADALTLERGRLVDMMLDSHTWLHGKKFGLYGDPDFVMGLTRFLLELGCEPTVILSHNANKRWQKAMNKMLDASPYGRDSEVFINCDLWHFRSLMFTRQPDFMIGNSYGKFIQRDTLAKGKAFEVPLIRLGFPLFDRHHLHRQTTWGYEGAMNIVTTLVNAVLEKLDSDTSQLGKTDYSFDLVR 519
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 14)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)
(-)
Klebsiella pneumoniae. Organism_taxid: 573. Strain: m5a1. Variant: wild-type. (3)
1a1qguA02A:62-204
1b1qguC02C:62-204
1c1qguA03A:205-318
1d1qguC03C:205-318
1e1qguB03B:361-466
1f1qguD03D:361-466
1g1qguB02B:212-316
1h1qguD02D:212-316
1i1qguA01A:1-61,A:343-477
1j1qguC01C:1-61,C:343-477
1k1qguB01B:68-211
1l1qguD01D:68-211
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3364] (10)
(-)
Clan: no clan defined [family: Oxidored_nitro] (12)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (NIFD_KLEPN | P00466)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0018697    carbonyl sulfide nitrogenase activity    Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
    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:0016163    nitrogenase activity    Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
    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:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
    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.
cellular component
    GO:0016612    molybdenum-iron nitrogenase complex    An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

Chain B,D   (NIFK_KLEPN | P09772)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0018697    carbonyl sulfide nitrogenase activity    Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
    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:0016163    nitrogenase activity    Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
    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:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
    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.
cellular component
    GO:0016612    molybdenum-iron nitrogenase complex    An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CFM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CLF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:446 - Pro A:447   [ RasMol ]  
    Gly C:446 - Pro C:447   [ RasMol ]  
    Phe B:467 - Pro B:468   [ RasMol ]  
    Phe D:467 - Pro D:468   [ RasMol ]  
    Trp A:251 - Ser A:252   [ RasMol ]  
    Trp C:251 - Ser C:252   [ RasMol ]  
    Tyr B:11 - Pro B:12   [ RasMol ]  
    Tyr D:11 - Pro D:12   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1qgu
    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
  NIFD_KLEPN | P00466
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NIFK_KLEPN | P09772
    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)
  1.18.6.1
    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
  NIFD_KLEPN | P00466
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NIFK_KLEPN | P09772
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NIFD_KLEPN | P00466: 1h1l 1qh1 1qh8
        NIFK_KLEPN | P09772: 1h1l 1qh1 1qh8

(-) Related Entries Specified in the PDB File

1qh1 1qh8