1FHF - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF SOYBEAN PEROXIDASE

Authors :   A. Henriksen, O. Mirza, C. Indiana, K. Welinder, K. Teilum, M. Gajhede

Date :   01 Aug 00 (Deposition) - 14 Feb 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

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

Reference :   A. Henriksen, O. Mirza, C. Indiani, K. Teilum, G. Smulevich, K. G. Welinder, M. Gajhede
Structure Of Soybean Seed Coat Peroxidase: A Plant Peroxidase With Unusual Stability And Haem-Apoprotein Interactions.
Protein Sci. V. 10 108 2001
PubMed-ID: 11266599 | Reference-DOI: 10.1110/PS.37301
(for further references see the PDB file header)

Molecule 1 - SEED COAT PEROXIDASE
	Chains	:	A, B, C
	EC Number	:	1.11.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	SOYBEAN
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TRS	6	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , VAL A:53	BINDING SITE FOR RESIDUE CA A 501
02	AC2	SOFTWARE	THR A:170 , ASP A:221 , THR A:224 , GLN A:227 , ASP A:229	BINDING SITE FOR RESIDUE CA A 502
03	AC3	SOFTWARE	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , VAL B:53	BINDING SITE FOR RESIDUE CA B 501
04	AC4	SOFTWARE	THR B:170 , ASP B:221 , THR B:224 , GLN B:227 , ASP B:229	BINDING SITE FOR RESIDUE CA B 502
05	AC5	SOFTWARE	ASP C:43 , VAL C:46 , GLY C:48 , ASP C:50 , SER C:52 , VAL C:53	BINDING SITE FOR RESIDUE CA C 501
06	AC6	SOFTWARE	THR C:170 , ASP C:221 , THR C:224 , GLN C:227 , ASP C:229	BINDING SITE FOR RESIDUE CA C 502
07	AC7	SOFTWARE	ARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , PRO A:139 , PHE A:152 , LEU A:165 , HIS A:169 , PHE A:171 , GLY A:172 , ARG A:173 , ALA A:174 , ARG A:175 , THR A:178 , SER A:245 , HOH A:1004	BINDING SITE FOR RESIDUE HEM A 350
08	AC8	SOFTWARE	PHE A:23 , PRO A:141 , HOH A:1003	BINDING SITE FOR RESIDUE TRS A 2001
09	AC9	SOFTWARE	THR A:85 , GLU A:88 , ASN A:89 , LEU A:297	BINDING SITE FOR RESIDUE TRS A 2002
10	BC1	SOFTWARE	ARG B:31 , ALA B:34 , SER B:35 , ARG B:38 , PHE B:41 , SER B:73 , PRO B:139 , PHE B:152 , LEU B:165 , HIS B:169 , PHE B:171 , GLY B:172 , ARG B:173 , ALA B:174 , ARG B:175 , THR B:178 , SER B:245 , HOH B:3004	BINDING SITE FOR RESIDUE HEM B 350
11	BC2	SOFTWARE	PHE B:23 , PRO B:141 , HOH B:3003	BINDING SITE FOR RESIDUE TRS B 4001
12	BC3	SOFTWARE	THR B:85 , GLU B:88 , ASN B:89 , LEU B:297	BINDING SITE FOR RESIDUE TRS B 4002
13	BC4	SOFTWARE	ARG C:31 , ALA C:34 , SER C:35 , ARG C:38 , PHE C:41 , SER C:73 , PRO C:139 , PHE C:152 , LEU C:165 , HIS C:169 , PHE C:171 , GLY C:172 , ARG C:173 , ALA C:174 , ARG C:175 , THR C:178 , SER C:245 , HOH C:5004	BINDING SITE FOR RESIDUE HEM C 350
14	BC5	SOFTWARE	PHE C:23 , PRO C:141 , HOH C:5003	BINDING SITE FOR RESIDUE TRS C 6001
15	BC6	SOFTWARE	THR C:85 , GLU C:88 , ASN C:89 , LEU C:297	BINDING SITE FOR RESIDUE TRS C 6002

Asymmetric Unit

No.	Residues
1	A:11	-	A:91
2	A:44	-	A:49
3	A:97	-	A:299
4	A:176	-	A:208
5	B:11	-	B:91
6	B:44	-	B:49
7	B:97	-	B:299
8	B:176	-	B:208
9	C:11	-	C:91
10	C:44	-	C:49
11	C:97	-	C:299
12	C:176	-	C:208

(no "Cis Peptide Bond" information available for 1FHF)

(no "SAP(SNP)/Variant" information available for 1FHF)

(no "PROSITE Motif" information available for 1FHF)

(no "Exon" information available for 1FHF)

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:304
 aligned with O22443_SOYBN | O22443 from UniProtKB/TrEMBL  Length:352

    Alignment length:304
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
         O22443_SOYBN    27 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 330
               SCOP domains d1fhfa_ A: Plant peroxidase                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1fhfA01 A:2-138,A:283-303  [code=1.10.520.10, no name defined]                                                                           1fhfA02 A:139-282 Peroxidase, domain 2                                                                                                          1fhfA01              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..................hhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.eee.hhhhhhh.hhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fhf A   1 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with O22443_SOYBN | O22443 from UniProtKB/TrEMBL  Length:352

    Alignment length:304
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
         O22443_SOYBN    27 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 330
               SCOP domains d1fhfb_ B: Plant peroxidase                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1fhfB01 B:2-138,B:283-303  [code=1.10.520.10, no name defined]                                                                           1fhfB02 B:139-282 Peroxidase, domain 2                                                                                                          1fhfB01              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..................hhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.eee.hhhhhhh.hhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fhf B   1 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain C from PDB  Type:PROTEIN  Length:304
 aligned with O22443_SOYBN | O22443 from UniProtKB/TrEMBL  Length:352

    Alignment length:304
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
         O22443_SOYBN    27 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 330
               SCOP domains d1fhfc_ C: Plant peroxidase                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1fhfC01 C:2-138,C:283-303  [code=1.10.520.10, no name defined]                                                                           1fhfC02 C:139-282 Peroxidase, domain 2                                                                                                          1fhfC01              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..................hhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.eee.hhhhhhh.hhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fhf C   1 QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: CCP-like (292)

Protein domain: Plant peroxidase (35)

Soybean (Glycine max) [TaxId: 3847] (1)

1a	d1fhfa_	A:
1b	d1fhfb_	B:
1c	d1fhfc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Peroxidase; domain 1 (244)

Homologous Superfamily: [code=1.10.520.10, no name defined] (241)

Soybean (Glycine max) (22)

1a	1fhfA01	A:2-138,A:283-303
1b	1fhfB01	B:2-138,B:283-303
1c	1fhfC01	C:2-138,C:283-303

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Soybean (Glycine max) (22)

2a	1fhfA02	A:139-282
2b	1fhfB02	B:139-282
2c	1fhfC02	C:139-282

(no "Pfam Domain" information available for 1FHF)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (O22443_SOYBN | O22443)

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:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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:0042744	hydrogen peroxide catabolic process	The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
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	1fhf
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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