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(-) Description

Title :  DEHALOPEROXIDASE B IN COMPLEX WITH SUBSTRATE P-NITROPHENOL
 
Authors :  L. Carey, R. Ghiladi
Date :  10 Jul 15  (Deposition) - 27 Apr 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Substrate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. L. Mccombs, J. D'Antonio, D. A. Barrios, L. M. Carey, R. A. Ghiladi
Nonmicrobial Nitrophenol Degradation Via Peroxygenase Activity Of Dehaloperoxidase-Hemoglobin From Amphitrite Ornata.
Biochemistry V. 55 2465 2016
PubMed-ID: 27070125  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00143

(-) Compounds

Molecule 1 - DEHALOPEROXIDASE B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AMPHITRITE ORNATA
    Organism Taxid: 129555

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NPO2Ligand/IonP-NITROPHENOL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NPO1Ligand/IonP-NITROPHENOL
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NPO1Ligand/IonP-NITROPHENOL
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:24 , GLU A:31 , ASN 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 , LEU A:127 , NPO A:204 , HOH A:337binding site for residue HEM A 201
2AC2SOFTWARELYS A:32 , GLY A:40 , HOH A:329 , GLY B:1 , PHE B:2 , LYS B:3 , HOH B:329 , HOH B:379binding site for residue SO4 A 202
3AC3SOFTWAREGLN A:4 , ASP A:5 , THR A:8 , SER A:114 , PHE A:115 , HOH A:321 , ASN B:26 , HOH B:305binding site for residue GOL A 203
4AC4SOFTWAREPHE A:21 , PHE A:35 , TYR A:38 , HIS A:55 , THR A:56 , VAL A:59 , PHE A:60 , HEM A:201binding site for residue NPO A 204
5AC5SOFTWAREHIS 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 , NPO B:204 , HOH B:313binding site for residue HEM B 201
6AC6SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , HOH A:317 , HOH A:328 , VAL B:39 , GLY B:40 , HOH B:317 , HOH B:321binding site for residue SO4 B 202
7AC7SOFTWARELYS B:51 , HIS B:55 , HOH B:301 , HOH B:334binding site for residue GOL B 203
8AC8SOFTWAREPHE B:21 , PHE B:35 , TYR B:38 , HIS B:55 , THR B:56 , VAL B:59 , PHE B:60 , HEM B:201binding site for residue NPO B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CHQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CHQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CHQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CHQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5CHQ)

(-) 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:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- 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
                 5chq A   1 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5chq B   1 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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  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 5CHQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CHQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CHQ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        Q9NAV7_9ANNE | Q9NAV7: 5k1l
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        Q9NAV7_9ANNE | Q9NAV7: 3ixf 5chr

(-) Related Entries Specified in the PDB File

5chr