3RIV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR PEROXIDASE

Authors :   V. S. Jasion, H. Li, T. L. Poulos

Date :   14 Apr 11 (Deposition) - 11 May 11 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Alpha Helical Bundle, Heme Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. S. Jasion, J. A. Polanco, Y. T. Meharenna, H. Li, T. L. Poulos
Crystal Structure Of Leishmania Major Peroxidase And Characterization Of The Compound I Tryptophan Radical.
J. Biol. Chem. V. 286 24608 2011
PubMed-ID: 21566139 | Reference-DOI: 10.1074/JBC.M111.230524

Molecule 1 - ASCORBATE PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPAL7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL CATALYTIC DOMAIN (UNP RESIDUES 35-303)
	Gene	:	APX, LMJF_34_0070
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	347515

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:60 , SER A:61 , ARG A:64 , TRP A:67 , PRO A:162 , GLY A:164 , VAL A:171 , LEU A:188 , ALA A:191 , HIS A:192 , GLY A:195 , GLU A:196 , CYS A:197 , HIS A:198 , PHE A:201 , SER A:202 , TRP A:208 , SER A:252 , PHE A:284 , HOH A:310 , HOH A:361 , HOH A:362 , HOH A:426	BINDING SITE FOR RESIDUE HEM A 305
2	AC2	SOFTWARE	THR A:193 , THR A:209 , ASP A:211 , GLY A:214 , ASP A:216 , SER A:218 , HOH A:537	BINDING SITE FOR RESIDUE K A 306
3	AC3	SOFTWARE	GLU A:69 , SER A:72 , SER A:81 , SER A:86 , GLU A:92	BINDING SITE FOR RESIDUE CA A 308
4	AC4	SOFTWARE	PRO B:60 , SER B:61 , TRP B:67 , PRO B:162 , GLY B:164 , VAL B:171 , LEU B:188 , ALA B:191 , HIS B:192 , GLY B:195 , GLU B:196 , CYS B:197 , HIS B:198 , PHE B:201 , SER B:202 , TRP B:208 , SER B:252 , PHE B:280 , HOH B:346 , HOH B:394 , HOH B:457 , HOH B:617	BINDING SITE FOR RESIDUE HEM B 305
5	AC5	SOFTWARE	THR B:193 , THR B:209 , ASP B:211 , GLY B:214 , ASP B:216 , SER B:218 , HOH B:413	BINDING SITE FOR RESIDUE K B 307
6	AC6	SOFTWARE	GLU B:69 , SER B:72 , GLY B:80 , SER B:81 , SER B:86 , GLU B:92	BINDING SITE FOR RESIDUE CA B 309

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

Asymmetric Unit

No.	Residues
1	Lys A:90	-	Pro A:91
2	Lys B:90	-	Pro B:91

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

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

(no "Exon" information available for 3RIV)

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:267
 aligned with Q4Q3K2_LEIMA | Q4Q3K2 from UniProtKB/TrEMBL  Length:303

    Alignment length:267
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       
         Q4Q3K2_LEIMA    34 VEEPPFDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPDGRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDNSFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFNKDFANAFKKLTELGTRNLHKAPA 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......ee......hhhhh...........hhhhhhhhhhhhh.hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eee........eee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3riv A  34 SEEPPFDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPDGRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDNSFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFNKDFANAFKKLTELGTRNLHKAPA 300
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with Q4Q3K2_LEIMA | Q4Q3K2 from UniProtKB/TrEMBL  Length:303

    Alignment length:265
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
         Q4Q3K2_LEIMA    34 VEEPPFDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPDGRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDNSFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFNKDFANAFKKLTELGTRNLHKA 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------peroxidase-3rivB01 B:44-272                                                                                                                                                                                                          -------------------------- Pfam domains (1)
           Pfam domains (2) ----------peroxidase-3rivB02 B:44-272                                                                                                                                                                                                          -------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......ee......hhhhh...........hhhhhhhhhhhhh.hhhhhhhhhhhhhh.eehhhhhh..ee.........hhhhhhhhhh.eee........eee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3riv B  34 SEEPPFDIRALRADIEDMISEKLELGPSLIRLAWHEAASYDCFKKDGSPNSASMRFKPECLYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIEYMGGPTIPFCWGRVDAKDGSVCGPDGRLPDGSKTQSHVREVFRRLGFNDQETVALIGAHTCGECHIEFSGYHGPWTHDKNGFDNSFFTQLLDEDWVLNPKVEQMQLMDRATTKLMMLPSDVCLLLDPSYRKYVELYAKDNDRFNKDFANAFKKLTELGTRNLHKA 298
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293

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 '\|'

(no "SCOP Domain" information available for 3RIV)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: peroxidase] (92)

Family: peroxidase (92)

Leishmania major (2)

1a	peroxidase-3rivB01	B:44-272
1b	peroxidase-3rivB02	B:44-272

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q4Q3K2_LEIMA | Q4Q3K2)

molecular function
	GO:0008447	L-ascorbate oxidase activity	Catalysis of the reaction: 2 L-ascorbate + O2 = 2 dehydroascorbate + 2 H2O.
	GO:0016688	L-ascorbate peroxidase activity	Catalysis of the reaction: L-ascorbate + hydrogen peroxide = dehydroascorbate + 2 H2O.
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0004447	iodide peroxidase activity	Catalysis of the reaction: iodide + hydrogen peroxide = iodine + 2 H2O.
	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:0055074	calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
	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:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0042744	hydrogen peroxide catabolic process	The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	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:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	GO:0042493	response to drug	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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	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.
	GO:0000302	response to reactive oxygen species	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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
	GO:0030322	stabilization of membrane potential	The accomplishment of a non-fluctuating membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0031304	intrinsic component of mitochondrial inner membrane	The component of the mitochondrial inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:90 - Pro A:91	[ RasMol ]
		Lys B:90 - Pro B:91	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3riv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q4Q3K2_LEIMA \| Q4Q3K2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	1.11.1.11
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q4Q3K2_LEIMA \| Q4Q3K2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q4Q3K2_LEIMA \| Q4Q3K2	:	3riw 4ged 5al9 5ala 5amm

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (21, 21)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File