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

(-) Description

Title :  CRYSTAL STRUCTURE OF BIPHENYL 2,3-DIOXYGENASE FROM SPHINGOMONAS YANOIKUYAE B1 BOUND TO BIPHENYL
 
Authors :  D. J. Ferraro, E. N. Brown, C. Yu, R. E. Parales, D. T. Gibson, S. Ramaswam
Date :  12 Mar 06  (Deposition) - 20 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rieske Oxygenase, Oxidoreductase, Non Heme Iron, Dioxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Ferraro, E. N. Brown, C. L. Yu, R. E. Parales, D. T. Gibson, S. Ramaswamy
Structural Investigations Of The Ferredoxin And Terminal Oxygenase Components Of The Biphenyl 2, 3-Dioxygenase From Sphingobium Yanoikuyae B1.
Bmc Struct. Biol. V. 7 10 2007
PubMed-ID: 17349044  |  Reference-DOI: 10.1186/1472-6807-7-10

(-) Compounds

Molecule 1 - BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET101D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BPHA1FA2F
    Organism Scientific: SPHINGOBIUM YANOIKUYAE
    Organism Taxid: 13690
    Strain: B1
 
Molecule 2 - BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT
    Chains: B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET101D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SPHINGOBIUM YANOIKUYAE
    Organism Taxid: 13690

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1BNL3Ligand/IonBIPHENYL
2FE3Ligand/IonFE (III) ION
3FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4ZN9Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:207 , HIS A:212 , ASP A:360 , HOH A:463BINDING SITE FOR RESIDUE FE A 456
02AC2SOFTWAREHIS C:207 , HIS C:212 , ASP C:360 , HOH C:460BINDING SITE FOR RESIDUE FE C 456
03AC3SOFTWAREHIS E:207 , HIS E:212 , ASP E:360 , HOH E:494BINDING SITE FOR RESIDUE FE E 456
04AC4SOFTWAREHIS B:19 , MET B:39 , HOH B:491BINDING SITE FOR RESIDUE ZN B 460
05AC5SOFTWAREHIS D:136 , HOH D:470 , HOH D:471 , HOH D:489BINDING SITE FOR RESIDUE ZN D 462
06AC6SOFTWAREHIS F:136 , HOH F:468 , HOH F:469BINDING SITE FOR RESIDUE ZN F 463
07AC7SOFTWAREHIS B:136 , HOH B:469 , HOH B:470 , HOH B:476BINDING SITE FOR RESIDUE ZN B 464
08AC8SOFTWAREHIS D:19 , HOH D:488BINDING SITE FOR RESIDUE ZN D 465
09AC9SOFTWAREHIS F:45 , HOH F:470BINDING SITE FOR RESIDUE ZN F 466
10BC1SOFTWAREHIS F:19BINDING SITE FOR RESIDUE ZN F 467
11BC2SOFTWAREHIS B:45 , ARG B:155 , HOH B:495BINDING SITE FOR RESIDUE ZN B 468
12BC3SOFTWAREHIS D:45 , ARG D:155BINDING SITE FOR RESIDUE ZN D 469
13BC4SOFTWARECYS A:80 , HIS A:82 , ARG A:83 , ASN A:85 , CYS A:100 , TYR A:102 , HIS A:103 , TRP A:105BINDING SITE FOR RESIDUE FES A 455
14BC5SOFTWAREASN A:200 , ASP A:204 , VAL A:208 , LEU A:223 , LEU A:260 , HIS A:293 , ASN A:295BINDING SITE FOR RESIDUE BNL A 457
15BC6SOFTWARECYS C:80 , HIS C:82 , ARG C:83 , CYS C:100 , TYR C:102 , HIS C:103 , TRP C:105BINDING SITE FOR RESIDUE FES C 455
16BC7SOFTWAREASN C:200 , ASP C:204 , VAL C:208 , LEU C:223 , LEU C:260 , HIS C:293 , ASN C:295BINDING SITE FOR RESIDUE BNL C 458
17BC8SOFTWARECYS E:80 , HIS E:82 , ARG E:83 , ASN E:85 , CYS E:100 , TYR E:102 , HIS E:103 , TRP E:105BINDING SITE FOR RESIDUE FES E 455
18BC9SOFTWAREASN E:200 , ASP E:204 , VAL E:208 , LEU E:223 , LEU E:260 , HIS E:293 , ASN E:295 , LEU E:305BINDING SITE FOR RESIDUE BNL E 459

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gly A:183 -Pro A:184
2Phe A:299 -Pro A:300
3Asp B:94 -Pro B:95
4Gly C:183 -Pro C:184
5Phe C:299 -Pro C:300
6Asp D:94 -Pro D:95
7Gly E:183 -Pro E:184
8Phe E:299 -Pro E:300
9Asp F:94 -Pro F:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GBX)

(-) 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:449
 aligned with A2TC87_SPHYA | A2TC87 from UniProtKB/TrEMBL  Length:454

    Alignment length:449
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445         
         A2TC87_SPHYA     6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE 454
               SCOP domains d2gbxa1 A:6-152 automated matches                                                                                                                  d2gbxa2 A:153-454 automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeehhhhhhhhhhhhhhhhh.....eeeee........eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee....................eeeeeee..eeeee......hhhhhhh.hhhhhhhhhh.....eeeeeeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh......hhhhheeeee.....eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeee.....eeeeeeeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eee.......eee......eee.....hhhhhhhhhhhhhhhhh.hhhhhhh.............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx A   6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE 454
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445         


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with A2TC88_SPHYA | A2TC88 from UniProtKB/TrEMBL  Length:174

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
         A2TC88_SPHYA     5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
               SCOP domains d2gbxb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhh...hhhhhheeeeeeeeee...................eeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee....eeeeeeeeeeeeee...eeeeeeeeeeeeeee....eeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx B   5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174


Chain C from PDB  Type:PROTEIN  Length:446
 aligned with A2TC87_SPHYA | A2TC87 from UniProtKB/TrEMBL  Length:454

    Alignment length:446
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445      
         A2TC87_SPHYA     6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLN 451
               SCOP domains d2gbxc1 C:6-152 automated matches                                                                                                                  d2gbxc2 C:153-451 automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eee.hhh.hhhhhhhhhhhh.....eeeee........eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee....................eeeeeee..eeeee......hhhhhhh.hhhhhhhhhh.....eeeeeeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhheeeee.....eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee...eeee....eeeeeee.....eeeeeeeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eee.......eee......eee.....hhhhhhhhhhhhhhhhh.hhhhhhhh............hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx C   6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLN 451
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445      


Chain D from PDB  Type:PROTEIN  Length:170
 aligned with A2TC88_SPHYA | A2TC88 from UniProtKB/TrEMBL  Length:174

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
         A2TC88_SPHYA     5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
               SCOP domains d2gbxd_ D: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee...................eeeeehhhhhhhhhhhhhh..........eeeeeeeeeeeee....eeeeeeeeeeeeee...eeeeeeeeeeeeeee....eeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx D   5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174


Chain E from PDB  Type:PROTEIN  Length:449
 aligned with A2TC87_SPHYA | A2TC87 from UniProtKB/TrEMBL  Length:454

    Alignment length:449
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445         
         A2TC87_SPHYA     6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE 454
               SCOP domains d2gbxe1 E:6-152 automated matches                                                                                                                  d2gbxe2 E:153-454 automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeehhhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee....................eeeeeee..eeeee......hhhhhhh.hhhhhhhhhh.....eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhheeeee.....eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeee.....eeeeeeeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eee.......eee......eee.....hhhhhhhhhhhhhhhhh.hhhhhhh............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx E   6 TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE 454
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445         


Chain F from PDB  Type:PROTEIN  Length:170
 aligned with A2TC88_SPHYA | A2TC88 from UniProtKB/TrEMBL  Length:174

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
         A2TC88_SPHYA     5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
               SCOP domains d2gbxf_ F: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...................eeeeehhhhhhhhhhhhhh..........eeeeeeeeeeeeee...eeeeeeeeeeeeee...eeeeeeeeeeeeee......eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gbx F   5 QIPVTPDVHYDIEAHYRAEVRMFQTGQYREWLQGMVAEDIHYWMPIYEQRLTRDRRPDPTPDDAAIYNDDFGELKQRVERLYSGQVWMEDPPSKIRYFVSNVEAFEAGNGELDVLSNILVYRNRRQTEVTVHTLGREDKLRRDGNGFKVFRRKLILDARVTQDKNLYFFC 174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   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  (3, 9)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GBX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E   (A2TC87_SPHYA | A2TC87)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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: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.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016708    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one donor.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

Chain B,D,F   (A2TC88_SPHYA | A2TC88)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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.

 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
    BNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
    Asp B:94 - Pro B:95   [ RasMol ]  
    Asp D:94 - Pro D:95   [ RasMol ]  
    Asp F:94 - Pro F:95   [ RasMol ]  
    Gly A:183 - Pro A:184   [ RasMol ]  
    Gly C:183 - Pro C:184   [ RasMol ]  
    Gly E:183 - Pro E:184   [ RasMol ]  
    Phe A:299 - Pro A:300   [ RasMol ]  
    Phe C:299 - Pro C:300   [ RasMol ]  
    Phe E:299 - Pro E:300   [ 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
  2gbx
    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
  A2TC87_SPHYA | A2TC87
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  A2TC88_SPHYA | A2TC88
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  A2TC87_SPHYA | A2TC87
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  A2TC88_SPHYA | A2TC88
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A2TC87_SPHYA | A2TC87: 2gbw
        A2TC88_SPHYA | A2TC88: 2gbw

(-) Related Entries Specified in the PDB File

2gbw CRYSTAL STRUCTURE OF BIPHENYL 2,3-DIOXYGENASE FROM SPHINGOMONAS YANOIKUYAE B1