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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL DESUNDECAPEPTIDE NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES
 
Authors :  H. T. Li, T. Chang, W. C. Chang, C. J. Chen, M. Y. Liu, L. L. Gui, J. P. Zhang, X. M. An, W. R. Chang
Date :  30 Aug 05  (Deposition) - 20 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Beta Barrel Trimer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. T. Li, T. Chang, W. C. Chang, C. J. Chen, M. Y. Liu, L. L. Gui, J. P. Zhang, X. M. An, W. R. Chang
Crystal Structure Of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes
Biochem. Biophys. Res. Commun. V. 338 1935 2005
PubMed-ID: 16293231  |  Reference-DOI: 10.1016/J.BBRC.2005.09.199
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B, C, D, E, F
    EC Number: 1.7.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: E.COLI M15 (PREP4)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DESUNDECAPEPTIDE NITRITE REDUCTASE
    Organism Scientific: ACHROMOBACTER CYCLOCLASTES
    Organism Taxid: 223
    Synonym: CU-NIR

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2CU12Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:100 , HIS A:135 , HIS B:306 , CL B:601BINDING SITE FOR RESIDUE CU A 502
02AC2SOFTWAREHIS B:100 , HIS B:135 , CL B:602 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
03AC3SOFTWAREHIS A:306 , HIS C:100 , HIS C:135 , CL C:603BINDING SITE FOR RESIDUE CU C 502
04AC4SOFTWAREHIS D:100 , HIS D:135 , CL D:604 , HIS E:306BINDING SITE FOR RESIDUE CU D 502
05AC5SOFTWAREHIS E:100 , HIS E:135 , HIS F:306 , CL F:605BINDING SITE FOR RESIDUE CU E 502
06AC6SOFTWAREHIS D:306 , HIS F:100 , HIS F:135 , CL F:606BINDING SITE FOR RESIDUE CU F 502
07AC7SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU A 501
08AC8SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU B 501
09AC9SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU C 501
10BC1SOFTWAREHIS D:95 , CYS D:136 , HIS D:145 , MET D:150BINDING SITE FOR RESIDUE CU D 501
11BC2SOFTWAREHIS E:95 , CYS E:136 , HIS E:145 , MET E:150BINDING SITE FOR RESIDUE CU E 501
12BC3SOFTWAREHIS F:95 , CYS F:136 , HIS F:145 , MET F:150BINDING SITE FOR RESIDUE CU F 501
13BC4SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , CU A:502 , HIS B:255 , ILE B:257 , HIS B:306BINDING SITE FOR RESIDUE CL B 601
14BC5SOFTWAREHIS B:100 , HIS B:135 , CU B:502 , HIS C:255 , ILE C:257BINDING SITE FOR RESIDUE CL B 602
15BC6SOFTWAREHIS A:255 , ILE A:257 , HIS A:306 , ASP C:98 , HIS C:100 , HIS C:135 , CU C:502BINDING SITE FOR RESIDUE CL C 603
16BC7SOFTWAREHIS D:100 , HIS D:135 , CU D:502 , HIS E:255 , HIS E:306BINDING SITE FOR RESIDUE CL D 604
17BC8SOFTWAREHIS E:100 , HIS E:135 , CU E:502 , HIS F:255 , ILE F:257 , HIS F:306BINDING SITE FOR RESIDUE CL F 605
18BC9SOFTWAREHIS D:255 , ILE D:257 , HIS D:306 , ASP F:98 , HIS F:100 , HIS F:135 , CU F:502BINDING SITE FOR RESIDUE CL F 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AVF)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Pro A:22 -Pro A:23
2Val A:68 -Pro A:69
3Pro B:22 -Pro B:23
4Val B:68 -Pro B:69
5Pro C:22 -Pro C:23
6Val C:68 -Pro C:69
7Pro D:22 -Pro D:23
8Val D:68 -Pro D:69
9Pro E:22 -Pro E:23
10Val E:68 -Pro E:69
11Pro F:22 -Pro F:23
12Val F:68 -Pro F:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AVF)

(-) Exons   (0, 0)

(no "Exon" information available for 2AVF)

(-) 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:314
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:314
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    
            NIR_ACHCY    50 LPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGE 363
               SCOP domains d2avfa1 A:12-159 automated matches                                                                                                                  d2avfa2 A:160-325 automated matches                                                                                                                                    SCOP domains
               CATH domains 2avfA01 A:12-158 Cupredoxins -  blue copper proteins                                                                                               2avfA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.........eee..................eeeeeeee....eeeeeee....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf A  12 LPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGE 325
                                    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    


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:316
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358      
            NIR_ACHCY    49 TLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEW 364
               SCOP domains d2avfb1 B:11-159 automated matches                                                                                                                   d2avfb2 B:160-326 automated matches                                                                                                                                     SCOP domains
               CATH domains 2avfB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                2avfB02 B:159-326 Cupredoxins -  blue copper proteins                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee.........eee........hhhhhh....eeeeeeee....eeeeeee....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf B  11 TLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEW 326
                                    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      


Chain C from PDB  Type:PROTEIN  Length:316
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:316
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
            NIR_ACHCY    48 STLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGE 363
               SCOP domains d2avfc1 C:10-159 automated matches                                                                                                                    d2avfc2 C:160-325 automated matches                                                                                                                                    SCOP domains
               CATH domains 2avfC01 C:10-158 Cupredoxins -  blue copper proteins                                                                                                 2avfC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhh........eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf C  10 STLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGE 325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319      


Chain D from PDB  Type:PROTEIN  Length:320
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:320
                                    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
            NIR_ACHCY    43 APVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTG 362
               SCOP domains d2avfd1 D:5-159 automated matches                                                                                                                          d2avfd2 D:160-324 automated matches                                                                                                                                   SCOP domains
               CATH domains 2avfD01 D:5-158 Cupredoxins -  blue copper proteins                                                                                                       2avfD02 D:159-324 Cupredoxins -  blue copper proteins                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee.........eee........hhhhhh....eeeeeeee....eeeeeee....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf D   5 APVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTG 324
                                    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


Chain E from PDB  Type:PROTEIN  Length:315
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:315
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     
            NIR_ACHCY    48 STLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTG 362
               SCOP domains d2avfe1 E:10-159 automated matches                                                                                                                    d2avfe2 E:160-324 automated matches                                                                                                                                   SCOP domains
               CATH domains 2avfE01 E:10-158 Cupredoxins -  blue copper proteins                                                                                                 2avfE02 E:159-324 Cupredoxins -  blue copper proteins                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.......eeeee.............ee...eeeeeeee....eeeeeee....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..................hhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf E  10 STLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTG 324
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319     


Chain F from PDB  Type:PROTEIN  Length:323
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:323
                                    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   
            NIR_ACHCY    43 APVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWN 365
               SCOP domains d2avff1 F:5-159 automated matches                                                                                                                          d2avff2 F:160-327 automated matches                                                                                                                                      SCOP domains
               CATH domains 2avfF01 F:5-158 Cupredoxins -  blue copper proteins                                                                                                       2avfF02 F:159-327 Cupredoxins -  blue copper proteins                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee.........eee..................eeeeeeee....eeeeeee....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avf F   5 APVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWN 327
                                    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
   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  (1, 12)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Fold: Cupredoxin-like (545)
(-)
Superfamily: Cupredoxins (543)
(-)
Family: automated matches (57)
(-)
Protein domain: automated matches (57)
(-)
Achromobacter cycloclastes [TaxId: 223] (3)
1ad2avfa1A:12-159
1bd2avfd1D:5-159
1cd2avfd2D:160-324
1dd2avfe1E:10-159
1ed2avfe2E:160-324
1fd2avff1F:5-159
1gd2avff2F:160-327
1hd2avfa2A:160-325
1id2avfb1B:11-159
1jd2avfb2B:160-326
1kd2avfc1C:10-159
1ld2avfc2C:160-325

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Cupredoxins - blue copper proteins (420)
(-)
Achromobacter cycloclastes. Organism_taxid: 223. (5)
1a2avfA01A:12-158
1b2avfE01E:10-158
1c2avfD01D:5-158
1d2avfF01F:5-158
1e2avfD02D:159-324
1f2avfE02E:159-324
1g2avfA02A:159-325
1h2avfC02C:159-325
1i2avfB02B:159-326
1j2avfF02F:159-327
1k2avfB01B:11-158
1l2avfC01C:10-158

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AVF)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NIR_ACHCY | P25006)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050421    nitrite reductase (NO-forming) activity    Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 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:0019333    denitrification pathway    The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_ACHCY | P25006: 1kcb 1nia 1nib 1nic 1nid 1nie 1nif 1rzp 1rzq 2bw4 2bw5 2bwd 2bwi 2nrd 2y1a 5akr 5i6k 5i6l 5i6m 5i6n 5i6o 5i6p

(-) Related Entries Specified in the PDB File

1rzp CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH6.2
1rzq CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH5.0