5AG1 - 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 :   DYP-TYPE PEROXIDASE OF AURICULARIA AURICULA-JUDAE (AAUDYPI) WITH MESO-NITRATED HEME

Authors :   E. Strittmatter, K. Piontek, D. A. Plattner

Date :   27 Jan 15 (Deposition) - 02 Mar 16 (Release) - 02 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Oxidoreductase, Dyp, Fungal, Heme, Glycoprotein, Nitration (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Strittmatter, K. Piontek, D. A. Plattner
Crystallographic Trapping Of A Covalently Modified Heme In A Dye-Decolorizing Peroxidase
To Be Published
PubMed: search

Molecule 1 - DYE-DECOLORIZING PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.19
	Fragment	:	DYP-TYPE PEROXIDASE DOMAIN, RESIDUES 64-509
	Organism Common	:	EAR FUNGUS
	Organism Scientific	:	AURICULARIA AURICULA-JUDAE
	Organism Taxid	:	29892
	Other Details	:	INCLUDING THE TWO PROTEIN CHAINS, THE CO- FACTOR DELTA-MESO NITROHEME, CARBOHYDRATE MOLECULES, CACODYLATE, FORMATE, GLYCEROL, NITRITE, AND WATER MOLECULES.
	Other Details - Source	:	GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSM 11326
	Strain	:	SXM9-C021

		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 (6, 21)

No.	Name	Count	Type	Full Name
1	CAC	2	Ligand/Ion	CACODYLATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	GOL	8	Ligand/Ion	GLYCEROL
4	N7H	2	Ligand/Ion	DELTA-MESO NITROHEME
5	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	NO2	2	Ligand/Ion	NITRITE ION

Biological Unit 1 (6, 12)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL
4	N7H	1	Ligand/Ion	DELTA-MESO NITROHEME
5	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	NO2	1	Ligand/Ion	NITRITE ION

Biological Unit 2 (5, 9)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	FMT	-1	Ligand/Ion	FORMIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL
4	N7H	1	Ligand/Ion	DELTA-MESO NITROHEME
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	NO2	1	Ligand/Ion	NITRITE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:286 , HIS A:287 , ALA A:288 , HOH A:2375	BINDING SITE FOR RESIDUE CAC A1449
02	AC2	SOFTWARE	HIS B:287 , ALA B:288	BINDING SITE FOR RESIDUE CAC B1449
03	AC3	SOFTWARE	ASP A:126 , GLN A:130 , HOH A:2218 , HOH A:2474 , HOH A:2475 , SER B:152 , PRO B:339 , GOL B:1453	BINDING SITE FOR RESIDUE GOL A1450
04	AC4	SOFTWARE	LYS A:21 , SER A:152 , PRO A:339 , GLU A:340 , HOH A:2244 , HOH A:2410 , HOH A:2412 , ASP B:126 , ASP B:129 , GLN B:130	BINDING SITE FOR RESIDUE GOL B1450
05	AC5	SOFTWARE	ARG A:154 , GLU A:158 , PHE A:164 , GLY A:165 , ASN A:227 , LYS A:257 , HOH A:2307 , HOH A:2476	BINDING SITE FOR RESIDUE GOL A1451
06	AC6	SOFTWARE	ARG A:445 , PRO B:201 , ILE B:202 , THR B:203 , HOH B:2407	BINDING SITE FOR RESIDUE GOL B1451
07	AC7	SOFTWARE	ARG B:251 , SER B:294 , ASP B:295 , GLN B:296 , SER B:297 , GLY B:410 , LEU B:412 , PRO B:413 , SER B:416 , HOH B:2317	BINDING SITE FOR RESIDUE GOL B1452
08	AC8	SOFTWARE	GOL A:1450 , HOH A:2211 , SER B:150 , SER B:152 , TYR B:337 , GLY B:338 , HOH B:2180	BINDING SITE FOR RESIDUE GOL B1453
09	AC9	SOFTWARE	ALA A:272 , ASP A:276 , ARG A:279 , HOH A:2358	BINDING SITE FOR RESIDUE GOL A1452
10	BC1	SOFTWARE	GLY A:196 , ALA A:197 , THR A:198 , ASN A:199 , ASP A:200	BINDING SITE FOR RESIDUE GOL A1453
11	BC2	SOFTWARE	GLU A:162 , PHE A:166 , LEU A:167 , ASP A:168 , GLY A:169 , ILE A:170 , ALA A:171 , GLN A:221 , VAL A:253 , ARG A:255 , HIS A:304 , THR A:308 , ARG A:309 , ARG A:311 , ARG A:332 , LEU A:357 , PHE A:359 , PHE A:370 , ILE A:398 , NO2 A:1460 , HOH A:2339 , HOH A:2365 , HOH A:2372 , HOH A:2483	BINDING SITE FOR RESIDUE N7H A1458
12	BC3	SOFTWARE	GLU B:162 , PHE B:166 , LEU B:167 , ASP B:168 , GLY B:169 , ILE B:170 , ALA B:171 , LEU B:219 , GLN B:221 , VAL B:253 , ARG B:255 , HIS B:304 , THR B:308 , ARG B:309 , ARG B:311 , ARG B:332 , PHE B:359 , PHE B:370 , ILE B:398 , VAL B:426 , NO2 B:1457 , HOH B:2273 , HOH B:2302 , HOH B:2309 , HOH B:2409	BINDING SITE FOR RESIDUE N7H B1456
13	BC4	SOFTWARE	ASN A:30 , SER A:141	BINDING SITE FOR RESIDUE FMT A1459
14	BC5	SOFTWARE	ASP A:168 , ARG A:332 , LEU A:357 , PHE A:359 , N7H A:1458 , HOH A:2259	BINDING SITE FOR RESIDUE NO2 A1460
15	BC6	SOFTWARE	ASP B:168 , ARG B:332 , PHE B:359 , N7H B:1456 , HOH B:2201 , HOH B:2344	BINDING SITE FOR RESIDUE NO2 B1457
16	BC7	SOFTWARE	GLN A:278 , ASN A:282 , PRO A:320 , HOH A:2367 , HOH A:2477 , HOH A:2478	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1454 THROUGH NAG A1457 BOUND TO ASN A 282
17	BC8	SOFTWARE	LYS A:228 , ASP A:232 , ALA A:347 , ASN A:349 , HOH A:2309 , HOH A:2479	BINDING SITE FOR MONO-SACCHARIDE NAG A1455 BOUND TO ASN A 349
18	BC9	SOFTWARE	ASN A:415 , SER A:417 , HOH A:2459 , HOH A:2463 , HOH A:2480 , HOH A:2481 , HOH A:2482	BINDING SITE FOR MONO-SACCHARIDE NAG A1456 BOUND TO ASN A 415
19	CC1	SOFTWARE	GLN B:278 , ARG B:279 , ASN B:282 , PRO B:320 , HOH B:2304 , HOH B:2306 , HOH B:2408	BINDING SITE FOR MONO-SACCHARIDE NAG B1454 BOUND TO ASN B 282
20	CC2	SOFTWARE	LYS B:228 , ASP B:232 , ALA B:347 , ASN B:349 , HOH B:2352	BINDING SITE FOR MONO-SACCHARIDE NAG B1455 BOUND TO ASN B 349

(no "SS Bond" information available for 5AG1)

Asymmetric Unit

No.	Residues
1	Pro A:320	-	Pro A:321
2	Phe A:383	-	Pro A:384
3	Thr A:388	-	Pro A:389
4	Ala B:288	-	Gly B:289
5	Pro B:320	-	Pro B:321
6	Phe B:383	-	Pro B:384
7	Thr B:388	-	Pro B:389

(no "SAP(SNP)/Variant" information available for 5AG1)

(no "PROSITE Motif" information available for 5AG1)

(no "Exon" information available for 5AG1)

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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhh.............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ag1 A   3 SLNTDDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442

Chain B from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhh..eeeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhhh..........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhh.............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ag1 B   4 LNTDDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    13        23        33        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       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443

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 5AG1)

(no "CATH Domain" information available for 5AG1)

(no "Pfam Domain" information available for 5AG1)

Asymmetric Unit(hide GO term definitions)

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
		CAC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		N7H	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO2	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala B:288 - Gly B:289	[ RasMol ]
		Phe A:383 - Pro A:384	[ RasMol ]
		Phe B:383 - Pro B:384	[ RasMol ]
		Pro A:320 - Pro A:321	[ RasMol ]
		Pro B:320 - Pro B:321	[ RasMol ]
		Thr A:388 - Pro A:389	[ RasMol ]
		Thr B:388 - Pro B:389	[ 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
	5ag1
		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
	I2DBY1_AURAJ \| I2DBY1
		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)
	1.11.1.19
		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
	I2DBY1_AURAJ \| I2DBY1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	I2DBY1_AURAJ \| I2DBY1	:	4au9 4uzi 4w7j 4w7k 4w7l 4w7m 4w7n 4w7o 5ag0 5ikd 5ikg

5ag0	DYP-TYPE PEROXIDASE OF AURICULARIA AURICULA-JUDAE ( AAUDYPI) CRYSTALLIZED AT PH 6.5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 21)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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 (0, 0)

Gene Ontology (6, 6)

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