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(-) Description

Title :  CHARACTERIZATION OF THE INHIBITOR BINDING SITE OF THE DEHALOPEROXIDASE-HEMOGLOBIN FROM AMPHITRITE ORNATA USING HIGH-PRESSURE XENON DERIVATIZATION
 
Authors :  V. S. De Serrano, S. Franzen
Date :  23 Apr 10  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Globin, Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. S. De Serrano, S. Franzen
Characterization Of The Inhibitor Binding Site Of The Dehaloperoxidase-Hemoglobin From Amphitrite Ornata Using High-Pressure Xenon Derivatization
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEHALOPEROXIDASE A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHP A
    Organism Scientific: AMPHITRITE ORNATA
    Organism Taxid: 129555

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO44Ligand/IonSULFATE ION
3XE4Ligand/IonXENON

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:24 , GLU A:31 , TYR A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , MET A:63 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , HOH A:401 , HOH A:834BINDING SITE FOR RESIDUE HEM A 139
2AC2SOFTWARELEU A:62 , VAL A:66 , ASP A:79 , THR A:82BINDING SITE FOR RESIDUE XE A 182
3AC3SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , HOH A:220 , HOH A:239 , HOH A:297 , ARG B:32 , VAL B:39 , GLY B:40BINDING SITE FOR RESIDUE SO4 A 195
4AC4SOFTWAREARG A:32 , GLY A:40 , GLY B:1 , PHE B:2 , LYS B:3 , ASP B:116 , HOH B:232 , HOH B:255 , HOH B:321 , HOH B:520BINDING SITE FOR RESIDUE SO4 B 196
5AC5SOFTWARETYR A:28 , PRO A:29 , ASP A:30 , HOH A:323 , HOH A:380 , ARG B:33 , GLN B:118BINDING SITE FOR RESIDUE SO4 A 197
6AC6SOFTWARELYS A:99 , HOH A:429 , HOH A:503 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:480BINDING SITE FOR RESIDUE SO4 B 198
7AC7SOFTWAREPHE B:24 , GLU B:31 , TYR B:34 , PHE B:35 , HIS B:55 , LYS B:58 , VAL B:59 , MET B:63 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127 , HOH B:389 , HOH B:462 , HOH B:483 , HOH B:835BINDING SITE FOR RESIDUE HEM B 139
8AC8SOFTWAREPHE B:21BINDING SITE FOR RESIDUE XE B 183
9AC9SOFTWARELEU B:62 , ASP B:79BINDING SITE FOR RESIDUE XE B 184

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MOU)

(-) Exons   (0, 0)

(no "Exon" information available for 3MOU)

(-) 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:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3moua_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mou A   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3moub_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Globin-3mouB01 B:2-128                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) -Globin-3mouB02 B:2-128                                                                                                         --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mou B   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9NAV8_9ANNE | Q9NAV8)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9NAV8_9ANNE | Q9NAV8: 1ew6 1ewa 2qfk 2qfn 3dr9 3k3u 3kun 3kuo 3lb1 3lb2 3lb3 3lb4 3mym 3myn 3o7n 3oj1 3ok5 3ord 4dwt 4dwu 4fh6 4fh7 4gzg 4hsw 4hsx 4ilz 4jac 4jyq 4kjt 4kmv 4kmw 4kn3

(-) Related Entries Specified in the PDB File

3lb1 DEHALOPEROXIDASE-HEMOGLOBIN WITH INTERNALLY BOUND 4- IODOPHENOL INHIBITOR
3lb2 DEHALOPEROXIDASE-HEMOGLOBIN WITH INTERNALLY BOUND 4- BROMOPHENOL INHIBITOR
3lb3 DEHALOPEROXIDASE-HEMOGLOBIN WITH INTERNALLY BOUND 4- CHLOROPHENOL INHIBITOR
3lb4 DEHALOPEROXIDASE-HEMOGLOBIN WITH INTERNALLY BOUND 4- FLUOROPHENOL INHIBITOR