3OK5 - JenaLib

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Title :   STRUCTURE OF THE H55D MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A FROM AMPHITRITI ORNATA WITH 4-BROMOPHENOL INHIBITOR

Authors :   J. Zhao, V. S. De Serrano, S. Franzen

Date :   24 Aug 10 (Deposition) - 07 Sep 11 (Release) - 14 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

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

Reference :   J. Zhao, V. S. De Serrano, Franzen. S.
Effect Of The H55D Mutation On The Kinetics And Structure O Dehaloperoxidase-Hemoglobin A
To Be Published
PubMed: search

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
	Mutation	:	YES
	Organism Scientific	:	AMPHITRITE ORNATA
	Organism Taxid	:	129555

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BML	2	Ligand/Ion	4-BROMOPHENOL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	BML	1	Ligand/Ion	4-BROMOPHENOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	BML	1	Ligand/Ion	4-BROMOPHENOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	BML	1	Ligand/Ion	4-BROMOPHENOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:24 , GLU A:31 , TYR A:34 , PHE A:35 , ASP 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 , BML A:138	BINDING SITE FOR RESIDUE HEM A 139
2	AC2	SOFTWARE	PHE A:21 , PHE A:35 , TYR A:38 , ASP A:55 , THR A:56 , VAL A:59 , LEU A:100 , HEM A:139	BINDING SITE FOR RESIDUE BML A 138
3	AC3	SOFTWARE	TYR A:28 , PRO A:29 , ASP A:30 , HOH A:210 , ARG B:33 , GLN B:118	BINDING SITE FOR RESIDUE SO4 A 198
4	AC4	SOFTWARE	GLU B:31 , TYR B:34 , PHE B:35 , ASP 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 , BML B:138 , HOH B:330 , HOH B:449	BINDING SITE FOR RESIDUE HEM B 139
5	AC5	SOFTWARE	PHE B:21 , PHE B:35 , TYR B:38 , ASP B:55 , THR B:56 , VAL B:59 , LEU B:100 , HEM B:139	BINDING SITE FOR RESIDUE BML B 138
6	AC6	SOFTWARE	ARG A:32 , GLY A:40 , HOH A:489 , GLY B:1 , PHE B:2 , LYS B:3 , HOH B:236 , HOH B:614	BINDING SITE FOR RESIDUE SO4 B 195
7	AC7	SOFTWARE	GLY A:1 , PHE A:2 , LYS A:3 , HOH A:215 , HOH A:278 , HOH A:563 , ARG B:32 , VAL B:39 , GLY B:40	BINDING SITE FOR RESIDUE SO4 B 196
8	AC8	SOFTWARE	LYS A:99 , HOH A:382 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:621	BINDING SITE FOR RESIDUE SO4 B 197
9	AC9	SOFTWARE	LYS B:47 , ASN B:81 , THR B:82 , GLN B:85 , HOH B:300 , HOH B:323 , HOH B:412	BINDING SITE FOR RESIDUE SO4 B 199

(no "SS Bond" information available for 3OK5)

(no "Cis Peptide Bond" information available for 3OK5)

(no "SAP(SNP)/Variant" information available for 3OK5)

(no "PROSITE Motif" information available for 3OK5)

(no "Exon" information available for 3OK5)

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
 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 d3ok5a_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- 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
                 3ok5 A   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDDTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 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 d3ok5b_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ok5 B   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDDTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 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)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Dehaloperoxidase (30)

Amphitrite ornata [TaxId: 129555] (30)

1a	d3ok5a_	A:
1b	d3ok5b_	B:

(no "CATH Domain" information available for 3OK5)

(no "Pfam Domain" information available for 3OK5)

Asymmetric 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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2qfk	WILD-TYPE DEHALOPEROXIDASE-HEMOGLOBIN A
2qfn	OXYFERROUS C73S DEHALOPEROXIDASE-HEMOGLOBIN A
3dr9	DEOXY DEHALOPEROXIDASE-HEMOGLOBIN A
3ixf	DEHALOPEROXIDASE-HEMOGLOBIN B
3kuo	METCYANO DEHALOPEROXIDASE-HEMOGLOBIN A
3oj1	H55D MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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