1V5E - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PYRUVATE OXIDASE CONTAINING FAD, FROM AEROCOCCUS VIRIDANS

Authors :   M. T. Hossain, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Take

Date :   22 Nov 03 (Deposition) - 28 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

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

Reference :   M. T. Hossain, K. Suzuki, T. Yamamoto, S. Imamura, T. Sekiguchi, A. Takenaka
Crystal Structure Of Pyruvate Oxidase Containing Fad, From Aerococcus Viridans
To Be Published
PubMed: search

Molecule 1 - PYRUVATE OXIDASE
	Chains	:	A
	EC Number	:	1.2.3.3
	Organism Scientific	:	AEROCOCCUS VIRIDANS
	Organism Taxid	:	1377

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 20)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	16	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:119 , ASN A:120 , HIS A:127 , ARG A:133 , HOH A:1710 , HOH A:1747 , HOH A:1752 , HOH A:2069 , HOH A:2235 , HOH A:2285	BINDING SITE FOR RESIDUE SO4 A 1603
2	AC2	SOFTWARE	VAL A:335 , GLU A:336 , GLU A:337 , HOH A:1860	BINDING SITE FOR RESIDUE SO4 A 1604
3	AC3	SOFTWARE	ARG A:209 , LEU A:586 , GLU A:587 , HOH A:1778 , HOH A:2090	BINDING SITE FOR RESIDUE SO4 A 1605
4	AC4	SOFTWARE	GLY A:390 , GLY A:441 , ASP A:442 , GLY A:443 , ALA A:444 , HOH A:1657 , HOH A:1777 , HOH A:1795 , HOH A:2081	BINDING SITE FOR RESIDUE SO4 A 1606
5	AC5	SOFTWARE	PHE A:116 , GLY A:215 , ILE A:216 , GLY A:217 , THR A:239 , GLY A:240 , LYS A:241 , THR A:257 , TYR A:258 , ARG A:259 , VAL A:260 , GLY A:279 , SER A:280 , ASN A:281 , PHE A:282 , PRO A:283 , PHE A:284 , ASP A:301 , ILE A:302 , ASP A:303 , MET A:306 , GLY A:319 , ASP A:320 , ALA A:321 , VAL A:389 , SER A:411 , PRO A:412 , ALA A:415 , HOH A:1691 , HOH A:1692 , HOH A:1725 , HOH A:1865 , HOH A:1879 , HOH A:1886	BINDING SITE FOR RESIDUE FAD A 1601

(no "SS Bond" information available for 1V5E)

(no "Cis Peptide Bond" information available for 1V5E)

(no "SAP(SNP)/Variant" information available for 1V5E)

(no "PROSITE Motif" information available for 1V5E)

(no "Exon" information available for 1V5E)

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:590
 aligned with A9X9K8_9LACT | A9X9K8 from UniProtKB/TrEMBL  Length:592

    Alignment length:590
                                    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       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
         A9X9K8_9LACT     3 DNKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKHEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAILGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAIAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYEPIAPAAQDIDAAVELLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEALTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDIDPAMLGKRHHADVAILGDAGLAIDEILNKVDAVEESAWWTANLKNIANWREYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLDSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK 592
               SCOP domains d1v5ea2 A:3-186 Pyruvate oxidase                                                                                                                                                        d1v5ea1 A:187-363 Pyruvate oxidase                                                                                                                                               d1v5ea3 A:364-592 Pyruvate oxidase                                                                                                                                                                                                    SCOP domains
               CATH domains 1v5eA01 A:3-185  [code=3.40.50.970, no name defined]                                                                                                                                   ----1v5eA02 A:190-354 TPP-binding domain                                                                                                                                 1v5eA03 A:355-544  [code=3.40.50.970, no name defined]                                                                                                                                        ------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhh.........eeee..hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh..........hhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.eee.hhh..hhhhh........hhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhh..eee...hhhhh......eeee.....hhhhhhhhhhh.eeeee.................eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eee.........hhhhhhhhhhhhh....eeeeeehhhhhhhh.hhhhhhhh....eeeeee.....hhhhh................hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhh......hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v5e A   3 DNKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKHEEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAILGSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAIAKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYAPIAPAAQDIDAAVELLNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEALTGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDIDPAMLGKRHHADVAILGDAALAIDEILNKVDAVEESAWWTANLKNIANWREYINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMTPKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVVTNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQGAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLDSKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK 592
                                    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       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.970, no name defined] (144)

Aerococcus viridans. Organism_taxid: 1377 (3)

1a	1v5eA03	A:355-544
1b	1v5eA01	A:3-185

Homologous Superfamily: TPP-binding domain (120)

Aerococcus viridans. Organism_taxid: 1377 (3)

1v5eA02

A:190-354

(no "Pfam Domain" information available for 1V5E)

Asymmetric Unit(hide GO term definitions)

Chain A (A9X9K8_9LACT | A9X9K8)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0047112	pyruvate oxidase activity	Catalysis of the reaction: H(+) + O(2) + phosphate + pyruvate = acetyl phosphate + CO(2) + H(2)O(2).
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
biological 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.

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
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v5e)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1v5e
		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
	A9X9K8_9LACT \| A9X9K8
		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)
	1.2.3.3
		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
	A9X9K8_9LACT \| A9X9K8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	A9X9K8_9LACT \| A9X9K8	:	2dji

1pox	THE SAME PROTEIN FROM LACTOBACILLUS PLANTARUM
1v5f	PYRUVATE OXIDASE COMPLEXED WITH FAD AND TPP
1v5g	PYRUVATE OXIDASE CONTAINING FAD AND TPP, AND SUBSTRATE PYRUVATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

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

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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