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(-) Description

Title :  NAPHTHALENE 1,2-DIOXYGENASE BOUND TO ETHYLPHENYLSULFIDE
 
Authors :  D. J. Ferraro, S. Ramaswamy
Date :  17 Oct 12  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Ferraro, S. Ramaswamy
Naphthalene 1, 2-Dioxygenase Bound To Ethylphenylsulfide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAPHTHALENE 1,2-DIOXYGENASE SUBUNIT ALPHA
    Chains: A
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG121
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DOXB, NC_004999.1
    Organism Scientific: PSEUDOMONAS SP. C18
    Organism Taxid: 69011
    Strain: NCIB 9816-4
    Synonym: NAPHTHALENE 1,2-DIOXYGENASE ISP ALPHA
 
Molecule 2 - NAPHTHALENE 1,2-DIOXYGENASE SUBUNIT BETA
    Chains: B
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG121
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DOXD, NC_004999.1
    Organism Scientific: PSEUDOMONAS SP. C18
    Organism Taxid: 69011
    Strain: NCIB 9816-4
    Synonym: NAPHTHALENE 1,2-DIOXYGENASE ISP BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
116M1Ligand/Ion(ETHYLSULFANYL)BENZENE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3FE1Ligand/IonFE (III) ION
4FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
116M3Ligand/Ion(ETHYLSULFANYL)BENZENE
2EDO24Ligand/Ion1,2-ETHANEDIOL
3FE-1Ligand/IonFE (III) ION
4FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5SO412Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:31 , PHE A:35 , ALA A:36 , MET A:59 , GLY A:60 , ILE A:61 , ASP A:62 , PHE A:152 , TYR A:376 , GLN A:377BINDING SITE FOR RESIDUE EDO A 1001
02AC2SOFTWAREHIS A:18 , VAL A:80 , CYS A:81 , ARG A:82 , SER A:381 , ASP A:382 , HOH A:1115 , HOH A:1160 , HOH A:1175BINDING SITE FOR RESIDUE EDO A 1002
03AC3SOFTWARELEU A:128 , ASN A:129 , LYS A:130 , LYS A:131 , HOH A:1352BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARECYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , HIS A:104 , TRP A:106BINDING SITE FOR RESIDUE FES A 1004
05AC5SOFTWAREHIS A:208 , HIS A:213 , ASP A:362 , HOH A:1251BINDING SITE FOR RESIDUE FE A 1005
06AC6SOFTWAREASN A:201 , ASP A:205 , VAL A:260 , HIS A:295 , ASN A:297 , LEU A:307 , HOH A:1596BINDING SITE FOR RESIDUE 16M A 1006
07AC7SOFTWARETYR B:87 , GLN B:101 , MET B:190 , VAL B:191 , PHE B:192 , HOH B:1113 , HOH B:1118 , HOH B:1286BINDING SITE FOR RESIDUE EDO B 1001
08AC8SOFTWAREASN B:90 , GLN B:93 , HOH B:1154 , HOH B:1217BINDING SITE FOR RESIDUE EDO B 1002
09AC9SOFTWAREALA B:157 , GLU B:159 , PHE B:176 , VAL B:177 , ASP B:178 , HOH B:1125 , HOH B:1303BINDING SITE FOR RESIDUE EDO B 1003
10BC1SOFTWAREPRO A:49 , ALA A:50 , ASP A:53 , HOH A:1211 , ARG B:77 , TYR B:78 , LYS B:79 , LEU B:80 , HOH B:1247 , HOH B:1314BINDING SITE FOR RESIDUE EDO B 1004
11BC2SOFTWAREGLN B:62 , GLN B:64 , HOH B:1175 , HOH B:1194 , HOH B:1240 , HOH B:1253BINDING SITE FOR RESIDUE SO4 B 1005
12BC3SOFTWAREGLY B:58 , SER B:59 , GLU B:60 , GLY B:165 , GLU B:166 , LYS B:171 , HOH B:1301BINDING SITE FOR RESIDUE SO4 B 1006
13BC4SOFTWAREPRO A:118 , PHE A:119 , HOH B:1210 , HOH B:1293BINDING SITE FOR RESIDUE EDO B 1007
14BC5SOFTWAREGLU B:82 , ALA B:83 , ASN B:85 , HOH B:1236 , HOH B:1258BINDING SITE FOR RESIDUE EDO B 1008
15BC6SOFTWARELYS A:245 , TRP A:439 , HIS A:440 , HOH B:1166 , HOH B:1188 , HOH B:1208BINDING SITE FOR RESIDUE SO4 B 1009

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:24 -B:24

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:184 -Pro A:185
2Phe A:301 -Pro A:302
3Ser B:110 -Pro B:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HM2)

(-) Exons   (0, 0)

(no "Exon" information available for 4HM2)

(-) 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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hm2a1 A:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d4hm2a2 A:155-446 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhh.eee.hhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee....eee..hhhhhh....hhhhh......eeeee..eeeee......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh.......eeeee.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........eee........ee.......eee.....hhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hm2 A   1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKT 446
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440      


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4hm2b_ B: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeeeee..............eeeeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hm2 B   2 INIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HM2)

(-) Gene Ontology  (13, 19)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NDOB_PSEU8 | P0A111: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm0 4hm1 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8
        NDOC_PSEU8 | P0A113: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm0 4hm1 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8

(-) Related Entries Specified in the PDB File

4hm0 4hm1 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8