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(-) Description

Title :  REDUCED AND CARBONMONOXIDE-BOUND CYTOCHROME C-DEPENDENT NITRIC OXIDE REDUCTASE (CNOR) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ANTIBODY FRAGMENT
 
Authors :  N. Sato, S. Ishii, T. Hino, H. Sugimoto, Y. Fukumori, Y. Shiro, T. Tosha
Date :  18 Jul 13  (Deposition) - 28 May 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  B,C,H,L
Keywords :  Metal-Binding, Membrane Protein, Immune System-Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Sato, S. Ishii, H. Sugimoto, T. Hino, Y. Fukumori, Y. Sako, Y. Shiro, T. Tosha
Structures Of Reduced And Ligand-Bound Nitric Oxide Reductase Provide Insights Into Functional Differences In Respiratory Enzymes
Proteins 2013
PubMed-ID: 24338896  |  Reference-DOI: 10.1002/PROT.24492
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIBODY FAB FRAGMENT LIGHT CHAIN
    ChainsL
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - ANTIBODY FAB FRAGMENT HEAVY CHAIN
    ChainsH
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - NITRIC OXIDE REDUCTASE SUBUNIT B
    ChainsB
    EC Number1.7.2.5
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid208964
    StrainPAO1
    SynonymNOR LARGE SUBUNIT, NITRIC OXIDE REDUCTASE CYTOCHROME B SUBUNIT
 
Molecule 4 - NITRIC OXIDE REDUCTASE SUBUNIT C
    ChainsC
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid208964
    StrainPAO1
    SynonymNOR SMALL SUBUNIT, NITRIC OXIDE REDUCTASE CYTOCHROME C SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit BCHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
110M2Ligand/IonDECYL 4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE
2CA1Ligand/IonCALCIUM ION
3CMO2Ligand/IonCARBON MONOXIDE
4FE1Ligand/IonFE (III) ION
5HEC1Ligand/IonHEME C
6HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:30 , ILE B:31 , GLY B:34 , MET B:37 , TYR B:41 , PHE B:53 , ARG B:57 , HIS B:60 , GLU B:135 , HIS B:349 , PHE B:352 , TYR B:353 , MET B:397 , ARG B:440 , GLY B:444 , PHE B:447 , HEM B:802 , CA B:808 , HOH B:916 , ALA C:72 , TYR C:73 , PHE C:74BINDING SITE FOR RESIDUE HEM B 801
2AC2SOFTWAREGLU B:135 , PHE B:136 , TRP B:203 , VAL B:210 , GLU B:211 , HIS B:258 , HIS B:259 , GLU B:280 , ALA B:322 , GLY B:326 , PHE B:327 , HIS B:329 , ASN B:335 , HIS B:339 , GLY B:340 , THR B:344 , HIS B:347 , ALA B:351 , PHE B:352 , ALA B:355 , HEM B:801 , CMO B:804 , CMO B:805 , CA B:808 , HOH B:905 , HOH B:926BINDING SITE FOR RESIDUE HEM B 802
3AC3SOFTWAREHIS B:207 , GLU B:211 , HIS B:258 , HIS B:259 , CMO B:804 , CMO B:805BINDING SITE FOR RESIDUE FE B 803
4AC4SOFTWAREGLU B:211 , HEM B:802 , FE B:803 , CMO B:805BINDING SITE FOR RESIDUE CMO B 804
5AC5SOFTWAREHIS B:207 , GLU B:211 , HIS B:258 , HIS B:259 , HEM B:802 , FE B:803 , CMO B:804BINDING SITE FOR RESIDUE CMO B 805
6AC6SOFTWARELEU B:270 , TRP B:271 , SER B:274 , TYR B:336 , TYR B:337 , 10M B:807 , ASN C:138 , GLN C:139 , PRO C:142BINDING SITE FOR RESIDUE 10M B 806
7AC7SOFTWAREMET B:328 , TYR B:337 , THR B:338 , MET B:417 , 10M B:806BINDING SITE FOR RESIDUE 10M B 807
8AC8SOFTWAREARG B:57 , GLU B:135 , HEM B:801 , HEM B:802 , HOH B:905 , GLY C:71 , TYR C:73BINDING SITE FOR RESIDUE CA B 808
9AC9SOFTWAREASN B:54 , CYS C:61 , CYS C:64 , HIS C:65 , ALA C:75 , PRO C:76 , LEU C:78 , ARG C:84 , ARG C:85 , TRP C:98 , ARG C:109 , ARG C:110 , MET C:112 , PRO C:113 , PHE C:115 , LEU C:125 , HOH C:307 , HOH C:314 , HOH C:316 , HOH C:345BINDING SITE FOR RESIDUE HEC C 201

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:151 -H:206
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:157 -Pro H:158
5Glu H:159 -Pro H:160
6Arg H:199 -Pro H:200
7Phe B:48 -Pro B:49
8Gln C:102 -Pro C:103
9Trp C:140 -Pro C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.NORB_PSEAE19-466  1B:19-458
2CYTCPS51007 Cytochrome c family profile.NORC_PSEAE47-133  1C:47-133
3COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.NORB_PSEAE203-259  1B:203-259

(-) Exons   (0, 0)

(no "Exon" information available for 3WFC)

(-) 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 B from PDB  Type:PROTEIN  Length:449
 aligned with NORB_PSEAE | Q59647 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:450
                                    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       329       339       349       359       369       379       389       399       409       419       429       439       449       459
           NORB_PSEAE    10 FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF 459
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------COX1  PDB: B:19-458 UniProt: 19-466                                                                                                                                                                                                                                                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: B:203-259 UniProt: 203-259                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wfc B  10 FASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRR-DYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSF 458
                                    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| |    308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458
                                                                                                                                                                                                                                                                                                                            300 |                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                              301                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with NORC_PSEAE | Q59646 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  
           NORC_PSEAE     5 FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMNIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG 146
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.ee..ee........hhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------CYTC  PDB: C:47-133 UniProt: 47-133                                                    ------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfc C   5 FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG 146
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  

Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee...........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfc H   1 EVQLQQSGTVLARPGASVKMSCKASGYSFTSYWMHWVKQRPGQGLEWIGAVYPGNSDTSYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCSRSSLDGYYVKNWCFDVWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTRPSQSITCNVAHPASSTKVDKKIEPRG 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfc L   1 DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

   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 3WFC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (NORB_PSEAE | Q59647)
molecular function
    GO:0004129    cytochrome-c oxidase activity    Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016966    nitric oxide reductase activity    Catalysis of the reaction: H(2)O + 2 ferricytochrome c + nitrous oxide = 2 H(+) + 2 ferrocytochrome c + 2 nitric oxide.
    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:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    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:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain C   (NORC_PSEAE | Q59646)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO: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.
biological process
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NORB_PSEAE | Q596473o0r 3wfb 3wfd 3wfe
        NORC_PSEAE | Q596463o0r 3wfb 3wfd 3wfe

(-) Related Entries Specified in the PDB File

3o0r 3wfb 3wfd 3wfe