1N4W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ PH 7.3 (STREPTOMYCES SP. SA-COO)

Authors :   A. Vrielink, P. I. Lario

Date :   01 Nov 02 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.92

Chains :   Asym./Biol. Unit : A

Keywords :   Flavoenzyme, Steroid Metabolism, Oxidoreductase, Atomic Resolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Lyubimov, P. I. Lario, I. Moustafa, A. Vrielink
Atomic Resolution Crystallography Reveals How Changes In Ph Shape The Protein Microenvironment
Nat. Chem. Biol. V. 2 259 2006
PubMed-ID: 16604066 | Reference-DOI: 10.1038/NCHEMBIO784

Molecule 1 - CHOLESTEROL OXIDASE
	Chains	:	A
	EC Number	:	1.1.3.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCO202
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CHOA
	Organism Scientific	:	STREPTOMYCES SP.
	Organism Taxid	:	74576
	Other Details	:	FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME
	Strain	:	SA-COO
	Synonym	:	CHOD

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MN	1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:159 , HOH A:1013 , HOH A:1300 , HOH A:1318	BINDING SITE FOR RESIDUE MN A 512
2	AC2	SOFTWARE	ILE A:16 , GLY A:17 , GLY A:19 , TYR A:20 , GLY A:21 , LEU A:39 , GLU A:40 , MET A:41 , TYR A:107 , GLY A:109 , ARG A:110 , GLY A:111 , GLY A:114 , GLY A:115 , ASN A:119 , GLY A:120 , GLY A:121 , MET A:122 , ILE A:218 , HIS A:248 , GLN A:249 , VAL A:250 , GLY A:288 , ALA A:289 , GLY A:290 , TYR A:446 , HIS A:447 , ASP A:474 , GLY A:475 , ASN A:485 , PRO A:486 , PHE A:487 , HOH A:541 , HOH A:572 , HOH A:599 , HOH A:605 , HOH A:615 , HOH A:629 , HOH A:686 , HOH A:701 , HOH A:964 , HOH A:965 , HOH A:1319	BINDING SITE FOR RESIDUE FAD A 510
3	AC3	SOFTWARE	LEU A:44 , ILE A:244 , HOH A:618 , HOH A:705	BINDING SITE FOR RESIDUE GOL A 511

(no "SS Bond" information available for 1N4W)

(no "Cis Peptide Bond" information available for 1N4W)

(no "SAP(SNP)/Variant" information available for 1N4W)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_1	PS00623	GMC oxidoreductases signature 1.	CHOD_STRS0	146-169	1	A:109-132

(no "Exon" information available for 1N4W)

Asymmetric/Biological 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:499
 aligned with CHOD_STRS0 | P12676 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:499
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535         
           CHOD_STRS0    46 GYVPAVVIGTGYGAAVSALRLGEAGVQTLMLEMGQLWNQPGPDGNIFCGMLNPDKRSSWFKNRTEAPLGSFLWLDVVNRNIDPYAGVLDRVNYDQMSVYVGRGVGGGSLVNGGMAVEPKRSYFEEILPRVDSSEMYDRYFPRANSMLRVNHIDTKWFEDTEWYKFARVSREQAGKAGLGTVFVPNVYDFGYMQREAAGEVPKSALATEVIYGNNHGKQSLDKTYLAAALGTGKVTIQTLHQVKTIRQTKDGGYALTVEQKDTDGKLLATKEISCRYLFLGAGSLGSTELLVRARDTGTLPNLNSEVGAGWGPNGNIMTARANHMWNPTGAHQSSIPALGIDAWDNSDSSVFAEIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAPAVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYHPLGGCVLGKATDDYGRVAGYKNLYVTDGSLIPGSVGVNPFVTITALAERNVERIIKQDVT 544
               SCOP domains d1n4wa1 A:9-318,A:451-507 Cholesterol oxidase of GMC family                                                                                                                                                                                                                                                           d1n4wa2 A:319-450 Cholesterol oxidase                                                                                               d1n4wa1 A:9-318,A:451-507                                 SCOP domains
               CATH domains 1n4wA01 A:9-155,A:216-322,A:385-405,A:443-507  [code=3.50.50.60, no name defined]                                                                  1n4wA02 A:156-215,A:323-384,A:406-442                       1n4wA01 A:9-155,A:216-322,A:385-405,A:443-507  [code=3.50.50.60, no name defined]                          1n4wA02 A:156-215,A:323-384,A:406-442                         1n4wA01              1n4wA02 A:156-215,A:323-384,A:406-4421n4wA01 A:9-155,A:216-322,A:385-405,A:443-507                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeee.....................hhhhh...........hhhhhhhhh.........eeeee....eeeee...hhhhhh........hhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhhh....ee.....hhhhhhhhhh.....hhhhh...............hhhhhhhhh..eeeee.eeeeeeee.....eeeeeeee.....eeeeeeeeeeeeee.hhhhhhhhhhhhhhhh...................eeeeee................eeeee.......eeeeee.........eeeeeeee......eeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..............ee..ee........................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------GMC_OXRED_1             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n4w A   9 GYVPAVVIGTGYGAAVSALRLGEAGVQTLMLEMGQLWNQPGPDGNIFCGMLNPDKRSSWFKNRTEAPLGSFLWLDVVNRNIDPYAGVLDRVNYDQMSVYVGRGVGGGSLVNGGMAVEPKRSYFEEILPRVDSSEMYDRYFPRANSMLRVNHIDTKWFEDTEWYKFARVSREQAGKAGLGTVFVPNVYDFGYMQREAAGEVPKSALATEVIYGNNHGKQSLDKTYLAAALGTGKVTIQTLHQVKTIRQTKDGGYALTVEQKDTDGKLLATKEISCRYLFLGAGSLGSTELLVRARDTGTLPNLNSEVGAGWGPNGNIMTARANHMWNPTGAHQSSIPALGIDAWDNSDSSVFAEIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAPAVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYHPLGGCVLGKATDDYGRVAGYKNLYVTDGSLIPGSVGVNPFVTITALAERNVERIIKQDVT 507
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Cholesterol Oxidase; domain 2 (20)

Homologous Superfamily: Cholesterol Oxidase; domain 2 (20)

Sa-coo (Streptomyces sp) (9)

1n4wA02

A:156-215,A:323-384,A:406-442

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Sa-coo (Streptomyces sp) (9)

1n4wA01

A:9-155,A:216-322,A:385-405,A:443-507

(no "Pfam Domain" information available for 1N4W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CHOD_STRS0 | P12676)

molecular function
	GO:0016995	cholesterol oxidase activity	Catalysis of the reaction: cholesterol + O2 = cholest-5-en-3-one + H2O2.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0004769	steroid delta-isomerase activity	Catalysis of the reaction: a 3-oxo-delta(5)-steroid = a 3-oxo-delta(4)-steroid.
biological process
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
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/Biological 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 ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n4w)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	1n4w
		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
	CHOD_STRS0 \| P12676
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.1.3.6
		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
	CHOD_STRS0 \| P12676
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1b4v	NATIVE ENZYME AT 1.5 A RESOLUTION
1b8s	E361Q MUTANT
1cbo	H447N MUTANT
1cc2	H447Q MUTANT
1ijh	N485L MUTANT
1n1p	ATOMIC RESOLUTION @ PH 7.4
1n4u	ATOMIC RESOLUTION @ PH 4.5
1n4v	ATOMIC RESOLUTION @ PH 5.8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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