3IXF - JenaLib

Title :   CRYSTAL STRUCTURE OF DEHALOPEROXIDASE B AT 1.58 AND STRUCTURAL CHARACTERIZATION OF THE AB DIMER FROM AMPHITRITE ORNATA

Authors :   V. S. De Serrano, J. D'Antonio, M. K. Thompson, S. Franzen, R. A. Ghilad

Date :   03 Sep 09 (Deposition) - 19 May 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (1x)

Keywords :   Peroxidase, Globin, Heme, Oxygen Transport, Transport, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. De Serrano, J. D'Antonio, S. Franzen, R. A. Ghiladi
Structure Of Dehaloperoxidase B At 1. 58 A Resolution And Structural Characterization Of The Ab Dimer From Amphitrite Ornata.
Acta Crystallogr. , Sect. D V. 66 529 2010
PubMed-ID: 20445228 | Reference-DOI: 10.1107/S0907444910004580

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:24 , GLU A:31 , ASN A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , LEU A:62 , MET A:63 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , LEU A:127 , OXY A:186 , HOH A:429 , HOH A:495 , HOH A:528	BINDING SITE FOR RESIDUE HEM A 139
2	AC2	SOFTWARE	PHE B:24 , GLU B:31 , ASN 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:363 , HOH B:418 , HOH B:602 , HOH B:603 , HOH B:608	BINDING SITE FOR RESIDUE HEM B 139
3	AC3	SOFTWARE	PHE A:21 , PHE A:35 , HIS A:55 , VAL A:59 , HEM A:139 , HOH A:429	BINDING SITE FOR RESIDUE OXY A 186
4	AC4	SOFTWARE	GLY A:1 , PHE A:2 , LYS A:3 , ASP A:116 , HOH A:266 , HOH A:346 , LYS B:32 , VAL B:39 , GLY B:40 , HOH B:569	BINDING SITE FOR RESIDUE SO4 A 195
5	AC5	SOFTWARE	LYS A:32 , VAL A:39 , GLY A:40 , HOH A:235 , HOH A:331 , GLY B:1 , PHE B:2 , LYS B:3 , HOH B:284 , HOH B:336	BINDING SITE FOR RESIDUE SO4 A 196
6	AC6	SOFTWARE	GLY A:95 , LYS A:99 , HOH A:250 , HOH A:291 , GLY B:95 , LYS B:99 , HOH B:584 , HOH B:629	BINDING SITE FOR RESIDUE SO4 A 197
7	AC7	SOFTWARE	GLN A:85 , LYS B:51 , HIS B:55 , HOH B:543 , HOH B:617	BINDING SITE FOR RESIDUE SO4 B 198
8	AC8	SOFTWARE	LYS A:51 , HIS A:55 , HOH A:495 , HOH A:528 , GLN B:85 , HOH B:444	BINDING SITE FOR RESIDUE SO4 A 199

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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 Q9NAV7_9ANNE | Q9NAV7 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV7_9ANNE     2 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3ixfa_ A: automated matches                                                                                                              SCOP domains
               CATH domains 3ixfA00 A:1-137 Globins                                                                                                                   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
                 3ixf 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
 aligned with Q9NAV7_9ANNE | Q9NAV7 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV7_9ANNE     2 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d3ixfb_ B: automated matches                                                                                                              SCOP domains
               CATH domains 3ixfB00 B:1-137 Globins                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixf B   1 GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9NAV7_9ANNE | Q9NAV7)

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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