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(-) Description

Title :  STRUCTURE OF THE THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE IN A COMPLEX WITH NITRITE
 
Authors :  K. M. Polyakov, K. M. Boyko, A. Slutsky, T. V. Tikhonova, A. N. Antipov, R. A. Zvyagilskaya, A. N. Popov, V. S. Lamzin, G. P. Bourenkov, V. O. Pop
Date :  06 May 08  (Deposition) - 12 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Cytochrome C Nitrite Reductase, Nrfa, Sulfite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Polyakov, K. M. Boyko, T. V. Tikhonova, A. Slutsky, A. N. Antipov, R. A. Zvyagilskaya, A. N. Popov, G. P. Bourenkov, V. S. Lamzin, V. O. Popov
High-Resolution Structural Analysis Of A Novel Octaheme Cytochrome C Nitrite Reductase From The Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens
J. Mol. Biol. V. 389 846 2009
PubMed-ID: 19393666  |  Reference-DOI: 10.1016/J.JMB.2009.04.037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EIGHT-HEME NITRITE REDUCTASE
    Chains: A, B
    Organism Scientific: THIOALKALIVIBRIO NITRATIREDUCENS
    Organism Taxid: 186931
    Strain: ALEN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 32)

Asymmetric Unit (6, 32)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2HEC16Ligand/IonHEME C
3NA2Ligand/IonSODIUM ION
4NO22Ligand/IonNITRITE ION
5PG46Ligand/IonTETRAETHYLENE GLYCOL
6PG62Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
Biological Unit 1 (4, 78)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HEC48Ligand/IonHEME C
3NA-1Ligand/IonSODIUM ION
4NO26Ligand/IonNITRITE ION
5PG418Ligand/IonTETRAETHYLENE GLYCOL
6PG66Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:1232 , HOH A:1233BINDING SITE FOR RESIDUE CA A 526
02AC2SOFTWAREPRO A:116 , HEC A:1006 , HEC A:1007 , HOH A:1048 , HOH A:1327 , HOH A:1386BINDING SITE FOR RESIDUE CA A 527
03AC3SOFTWAREARG A:131 , TYR A:303 , HIS A:361 , HEC A:1004 , HOH A:1013 , HOH A:1359BINDING SITE FOR RESIDUE NO2 A 528
04AC4SOFTWAREHOH A:1404 , HOH A:1405BINDING SITE FOR RESIDUE NA A 529
05AC5SOFTWAREGLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:1696 , HOH B:1697BINDING SITE FOR RESIDUE CA B 526
06AC6SOFTWAREPRO B:116 , HEC B:1006 , HEC B:1007 , HOH B:1512 , HOH B:1789 , HOH B:1845 , HOH B:2002BINDING SITE FOR RESIDUE CA B 527
07AC7SOFTWAREARG B:131 , TYR B:303 , HIS B:361 , HEC B:1004 , HOH B:1431 , HOH B:1818BINDING SITE FOR RESIDUE NO2 B 528
08AC8SOFTWAREHOH B:1863 , HOH B:1864 , HOH B:1994BINDING SITE FOR RESIDUE NA B 529
09AC9SOFTWAREHIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , CYS A:305 , HIS A:361 , ASN A:486 , NO2 A:528 , HEC A:1006 , HOH A:1013 , HOH A:1028 , HOH A:1145 , HOH A:1146 , HOH A:1152 , HOH A:1362BINDING SITE FOR RESIDUE HEC A 1004
10BC1SOFTWARECYS A:66 , HIS A:70 , GLN A:73 , PHE A:74 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , ALA A:290 , MET A:384 , LYS A:386 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:1003 , HOH A:1116 , HOH A:1229 , HOH A:1250 , HOH A:1445 , HOH A:1523 , HOH A:1531BINDING SITE FOR RESIDUE HEC A 1005
11BC2SOFTWARESER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , LYS A:188 , LEU A:225 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , CA A:527 , HEC A:1004 , HEC A:1007 , HOH A:1017 , HOH A:1035 , HOH A:1140BINDING SITE FOR RESIDUE HEC A 1006
12BC3SOFTWAREHIS A:300 , PHE A:367 , HIS A:372 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , PRO A:403 , ARG A:404 , ILE A:427 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , CA A:527 , HEC A:1006 , HOH A:1140 , HOH A:1141 , HOH A:1149 , HOH A:1153 , HOH A:1327 , HOH A:1353BINDING SITE FOR RESIDUE HEC A 1007
13BC4SOFTWAREASN A:141 , TRP A:142 , GLN A:143 , VAL A:371 , HIS A:372 , ASN A:375 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , PHE A:490 , HOH A:1413 , HOH A:1459 , HOH A:1461BINDING SITE FOR RESIDUE HEC A 1008
14BC5SOFTWARECYS A:14 , PHE A:15 , HIS A:18 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , THR A:59 , ILE A:193 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HEC A:1001 , HEC A:1003 , HOH A:1087 , HOH A:1335 , HOH A:1471BINDING SITE FOR RESIDUE HEC A 1002
15BC6SOFTWARELYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HEC A:1002 , HEC A:1005 , HOH A:1304 , HOH A:1347 , HOH A:1388 , HOH A:1434 , HOH A:1546 , HOH A:1567 , THR B:68 , HOH B:1472BINDING SITE FOR RESIDUE HEC A 1003
16BC7SOFTWAREGLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HEC A:1002 , HOH A:1089 , HOH A:1114 , HOH A:1470 , HOH A:1472BINDING SITE FOR RESIDUE HEC A 1001
17BC8SOFTWARELYS A:431 , HIS A:435 , HOH A:1408 , HOH A:1446BINDING SITE FOR RESIDUE PG4 A 1009
18BC9SOFTWARETYR A:309 , LEU A:311 , GLY A:314 , ARG A:348 , ALA A:355 , HOH A:1247 , HOH A:1298BINDING SITE FOR RESIDUE PG6 A 1010
19CC1SOFTWAREGLN A:138 , PHE A:139 , HOH A:1273 , HOH A:1536 , HOH A:1537BINDING SITE FOR RESIDUE PG4 A 1011
20CC2SOFTWAREARG A:153 , THR A:157 , ASN A:222BINDING SITE FOR RESIDUE PG4 A 1012
21CC3SOFTWAREHIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , VAL B:301 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , NO2 B:528 , HEC B:1006 , HOH B:1431 , HOH B:1492 , HOH B:1609 , HOH B:1610 , HOH B:1616 , HOH B:1940BINDING SITE FOR RESIDUE HEC B 1004
22CC4SOFTWARECYS B:66 , HIS B:70 , GLN B:73 , LEU B:225 , ASN B:226 , CYS B:227 , CYS B:230 , HIS B:231 , ALA B:290 , MET B:384 , LYS B:386 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:1003 , HEC B:1006 , HOH B:1580 , HOH B:1693 , HOH B:1714 , HOH B:1904 , HOH B:1968BINDING SITE FOR RESIDUE HEC B 1005
23CC5SOFTWARESER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , LYS B:188 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , CA B:527 , HEC B:1004 , HEC B:1005 , HEC B:1007 , HOH B:1481 , HOH B:1499 , HOH B:1604 , HOH B:2002BINDING SITE FOR RESIDUE HEC B 1006
24CC6SOFTWAREHIS B:300 , PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , PRO B:403 , ARG B:404 , ILE B:427 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , CA B:527 , HEC B:1006 , HOH B:1604 , HOH B:1605 , HOH B:1613 , HOH B:1617 , HOH B:1789 , HOH B:1812 , HOH B:2002BINDING SITE FOR RESIDUE HEC B 1007
25CC7SOFTWAREASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , ASN B:375 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , PG4 B:1012 , HOH B:1872 , HOH B:1924 , HOH B:1954BINDING SITE FOR RESIDUE HEC B 1008
26CC8SOFTWARECYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , HIS B:25 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HEC B:1001 , HEC B:1003 , HOH B:1551 , HOH B:1796BINDING SITE FOR RESIDUE HEC B 1002
27CC9SOFTWARETHR A:68 , LYS B:29 , HIS B:30 , VAL B:33 , HIS B:37 , ALA B:65 , CYS B:66 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HEC B:1002 , HEC B:1005 , HOH B:1440 , HOH B:1767 , HOH B:1807 , HOH B:1847 , HOH B:1893 , HOH B:1928BINDING SITE FOR RESIDUE HEC B 1003
28DC1SOFTWAREGLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , ALA B:41 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , SER B:50 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HEC B:1002 , HOH B:1553 , HOH B:1578 , HOH B:1796 , HOH B:1912 , HOH B:1916 , HOH B:1932BINDING SITE FOR RESIDUE HEC B 1001
29DC2SOFTWARETHR B:94 , HIS B:435 , HOH B:1867 , HOH B:1905BINDING SITE FOR RESIDUE PG4 B 1009
30DC3SOFTWARELEU B:311 , ASP B:313 , GLY B:314 , ARG B:348 , ALA B:355 , HOH B:1711 , HOH B:1934 , HOH B:1935BINDING SITE FOR RESIDUE PG6 B 1010
31DC4SOFTWAREPHE B:172BINDING SITE FOR RESIDUE PG4 B 1011
32DC5SOFTWARETRP B:142 , PHE B:367 , SER B:370 , VAL B:371 , HIS B:372 , PHE B:490 , HIS B:491 , ASN B:492 , PRO B:493 , ASP B:494 , HEC B:1008 , HOH B:1963BINDING SITE FOR RESIDUE PG4 B 1012

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D1I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D1I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D1I)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.NIR_THIND37-448
 		  2A:9-420
B:9-420
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.NIR_THIND37-448
 		  6A:9-420
B:9-420

(-) Exons   (0, 0)

(no "Exon" information available for 3D1I)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:519
 aligned with NIR_THIND | L0DSL2 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:519
                                    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       482       492       502       512       522       532       542         
            NIR_THIND    33 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 551
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhhh.hhhhhh.....hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.eee...................hhhhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....eee..ee......ee...hhh.eee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----MULTIHEME_CYTC  PDB: A:9-420 UniProt: 37-448                                                                                                                                                                                                                                                                                                                                                                                ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1i A   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 523
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514         


Chain B from PDB  Type:PROTEIN  Length:519
 aligned with NIR_THIND | L0DSL2 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:519
                                    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       482       492       502       512       522       532       542         
            NIR_THIND    33 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 551
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhhh.hhhhhh.....hhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhh.eee...................hhhhhh..........hhhhh...........hhhhhhh......hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....ee...ee......ee...hhhhhee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----MULTIHEME_CYTC  PDB: B:9-420 UniProt: 37-448                                                                                                                                                                                                                                                                                                                                                                                ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1i B   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 523
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514
   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  (0, 0)

(no "SCOP Domain" information available for 3D1I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D1I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D1I)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIR_THIND | L0DSL2)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042279    nitrite reductase (cytochrome, ammonia-forming) activity    Catalysis of the reaction: NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+.
    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:0097164    ammonium ion metabolic process    The chemical reactions and pathways involving the ammonium ion.
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_THIND | L0DSL2: 2ot4 2zo5 3f29 3fo3 3gm6 3lg1 3lgq 3mmo 3owm 3rkh 3s7w 3sce 3uu9 4l38 4l3x 4l3y 4l3z 4q0t 4q17 4q1o 4q4u 4q5b 4q5c

(-) Related Entries Specified in the PDB File

2ot4 2zo5