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(-) Description

Title :  STRUCTURE OF DHP A IN COMPLEX WITH 2,4,6-TRIBROMOPHENOL IN 10% DMSO
 
Authors :  V. S. De Serrano, S. Franzen
Date :  05 Jun 12  (Deposition) - 27 Mar 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peroxidase, Globin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhao, V. De Serrano, J. Zhao, P. Le, S. Franzen
Structural And Kinetic Study Of An Internal Substrate Binding Site In Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata.
Biochemistry V. 52 2427 2013
PubMed-ID: 23480178  |  Reference-DOI: 10.1021/BI301307F

(-) 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: 562
    Expression System Vector Type: PLASMID
    Gene: DHPA
    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  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OXY2Ligand/IonOXYGEN MOLECULE
4SO43Ligand/IonSULFATE ION
5TBP2Ligand/Ion2,4,6-TRIBROMOPHENOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:31 , TYR A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , MET A:63 , LEU A:83 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , TBP A:203 , OXY A:204BINDING SITE FOR RESIDUE HEM A 201
02AC2SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , HOH A:310 , HOH A:326 , HOH A:377 , ARG B:32 , VAL B:39 , GLY B:40 , HOH B:312BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREILE A:20 , PHE A:21 , PHE A:24 , PHE A:35 , VAL A:59 , PHE A:60 , MET A:63 , LEU A:100 , HEM A:201 , OXY A:204BINDING SITE FOR RESIDUE TBP A 203
04AC4SOFTWAREHIS A:55 , VAL A:59 , HEM A:201 , TBP A:203BINDING SITE FOR RESIDUE OXY A 204
05AC5SOFTWAREGLU 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 , TBP B:203 , OXY B:205 , HOH B:374BINDING SITE FOR RESIDUE HEM B 201
06AC6SOFTWAREARG A:32 , VAL A:39 , GLY A:40 , GLY B:1 , PHE B:2 , LYS B:3 , ASP B:116 , HOH B:317 , HOH B:329 , HOH B:348 , HOH B:387BINDING SITE FOR RESIDUE SO4 B 202
07AC7SOFTWAREPHE B:21 , PHE B:24 , PHE B:35 , VAL B:59 , MET B:63 , ASN B:96 , LYS B:99 , LEU B:100 , HEM B:201 , OXY B:205BINDING SITE FOR RESIDUE TBP B 203
08AC8SOFTWAREPHE B:35 , LYS B:36 , ASN B:37 , VAL B:39 , HOH B:341 , HOH B:430BINDING SITE FOR RESIDUE DMS B 204
09AC9SOFTWAREPHE B:21 , PHE B:35 , HIS B:55 , VAL B:59 , HEM B:201 , TBP B:203BINDING SITE FOR RESIDUE OXY B 205
10BC1SOFTWARELYS A:99 , HOH A:401 , HOH A:402 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:426 , HOH B:427BINDING SITE FOR RESIDUE SO4 B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FH6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FH6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FH6)

(-) Exons   (0, 0)

(no "Exon" information available for 4FH6)

(-) 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
                                                                                                                                                                         
               SCOP domains d4fh6a_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fh6 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
                                                                                                                                                                         
               SCOP domains d4fh6b_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fh6 B   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
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  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 4FH6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FH6)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 3mou 3mym 3myn 3o7n 3oj1 3ok5 3ord 4dwt 4dwu 4fh7 4gzg 4hsw 4hsx 4ilz 4jac 4jyq 4kjt 4kmv 4kmw 4kn3

(-) Related Entries Specified in the PDB File

4fh7