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(-) Description

Title :  DEHALOPEROXIDASE B IN COMPLEX WITH SUBSTRATE P-NITROCATECHOL
 
Authors :  L. Carey, R. Ghiladi
Date :  10 Jul 15  (Deposition) - 27 Apr 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
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  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
14NC2Ligand/Ion4-NITROCATECHOL
2GOL3Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4OXY1Ligand/IonOXYGEN MOLECULE
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
14NC1Ligand/Ion4-NITROCATECHOL
2GOL2Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4OXY1Ligand/IonOXYGEN MOLECULE
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
14NC1Ligand/Ion4-NITROCATECHOL
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4OXY-1Ligand/IonOXYGEN MOLECULE
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU 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 , 4NC A:204 , OXY A:205binding site for residue HEM A 201
02AC2SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , HOH A:336 , HOH A:371 , LYS B:32 , VAL B:39 , GLY B:40 , HOH B:301binding site for residue SO4 A 202
03AC3SOFTWARELYS A:32 , VAL A:39 , GLY A:40 , HOH A:313 , HOH A:318 , HOH A:389 , GLY B:1 , PHE B:2 , LYS B:3 , HOH B:309binding site for residue SO4 A 203
04AC4SOFTWAREPHE A:21 , PHE A:35 , TYR A:38 , PHE A:52 , HIS A:55 , THR A:56 , VAL A:59 , PHE A:60 , HEM A:201 , OXY A:205binding site for residue 4NC A 204
05AC5SOFTWAREHIS A:55 , VAL A:59 , HEM A:201 , 4NC A:204binding site for residue OXY A 205
06AC6SOFTWAREGLN A:4 , ASP A:5 , THR A:8 , GLN A:113 , SER A:114 , HOH B:304binding site for residue GOL A 206
07AC7SOFTWARESER A:42 , GLN A:44 , GLU A:45 , GLU A:65 , ARG A:69 , HOH A:301 , HOH A:303 , HOH A:305 , HOH A:338 , ALA B:7binding site for residue GOL A 207
08AC8SOFTWAREHIS B:55 , LYS B:58 , VAL B:59 , MET B:63 , LEU B:83 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127 , 4NC B:202binding site for residue HEM B 201
09AC9SOFTWAREPHE B:21 , PHE B:35 , TYR B:38 , PHE B:52 , HIS B:55 , THR B:56 , VAL B:59 , PHE B:60 , HEM B:201binding site for residue 4NC B 202
10AD1SOFTWARELYS A:99 , THR B:93 , LYS B:99 , HOH B:305binding site for residue GOL B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CHR)

(-) 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
                 5chr 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.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5chr B   1 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
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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 5CHR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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

(-) Related Entries Specified in the PDB File

5chq