1EL8 - 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)

Biological Unit 2 (Jmol Viewer)

Title :   COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLSELENO]CETATE

Authors :   M. A. Wagner, P. Trickey, Z. -W. Chen, F. S. Mathews, M. S. Jorns

Date :   13 Mar 00 (Deposition) - 06 Dec 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   M. A. Wagner, P. Trickey, Z. W. Chen, F. S. Mathews, M. S. Jorns
Monomeric Sarcosine Oxidase: 1. Flavin Reactivity And Activ Site Binding Determinants.
Biochemistry V. 39 8813 2000
PubMed-ID: 10913292 | Reference-DOI: 10.1021/BI000349Z
(for further references see the PDB file header)

Molecule 1 - SARCOSINE OXIDASE
	Chains	:	A, B
	EC Number	:	1.5.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell	:	DH1 CELLS
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	69000
	Strain	:	B-0618

		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 (4, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	MSF	2	Ligand/Ion	[METHYLSELENO]ACETATE
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	MSF	1	Ligand/Ion	[METHYLSELENO]ACETATE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	MSF	1	Ligand/Ion	[METHYLSELENO]ACETATE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:81 , ASN A:151 , ARG A:154 , HOH A:881	BINDING SITE FOR RESIDUE PO4 A 803
2	AC2	SOFTWARE	THR A:318 , PHE A:342 , SER A:343 , GLY A:344 , FAD A:400	BINDING SITE FOR RESIDUE CL A 804
3	AC3	SOFTWARE	HIS B:53 , LEU B:113 , THR B:114 , GLU B:141 , ASN B:143 , SER B:144 , HOH B:1094	BINDING SITE FOR RESIDUE PO4 B 812
4	AC4	SOFTWARE	HIS B:81 , ASN B:151 , ARG B:154 , HOH B:825 , HOH B:1036	BINDING SITE FOR RESIDUE PO4 B 813
5	AC5	SOFTWARE	TYR B:317 , THR B:318 , SER B:343 , GLY B:344 , FAD B:400 , HOH B:829	BINDING SITE FOR RESIDUE CL B 814
6	AC6	SOFTWARE	GLY A:10 , GLY A:12 , SER A:13 , MET A:14 , VAL A:32 , ASP A:33 , ALA A:34 , PHE A:35 , HIS A:39 , GLY A:42 , SER A:43 , HIS A:44 , ARG A:49 , ILE A:50 , THR A:171 , ARG A:172 , VAL A:173 , SER A:200 , MET A:201 , GLY A:202 , TRP A:204 , LEU A:208 , VAL A:225 , TYR A:254 , CYS A:315 , MET A:316 , TYR A:317 , PHE A:342 , GLY A:344 , HIS A:345 , GLY A:346 , PHE A:347 , LYS A:348 , MSF A:801 , CL A:804 , HOH A:806 , HOH A:808 , HOH A:815 , HOH A:900 , HOH A:929 , HOH A:1070	BINDING SITE FOR RESIDUE FAD A 400
7	AC7	SOFTWARE	ILE A:50 , ARG A:52 , MET A:245 , TYR A:254 , HIS A:269 , GLY A:344 , LYS A:348 , FAD A:400	BINDING SITE FOR RESIDUE MSF A 801
8	AC8	SOFTWARE	GLY B:10 , GLY B:12 , SER B:13 , MET B:14 , VAL B:32 , ASP B:33 , ALA B:34 , PHE B:35 , HIS B:39 , GLY B:42 , SER B:43 , HIS B:44 , ARG B:49 , ILE B:50 , THR B:171 , ARG B:172 , VAL B:173 , SER B:200 , MET B:201 , GLY B:202 , TRP B:204 , LEU B:208 , VAL B:225 , TYR B:254 , CYS B:315 , MET B:316 , TYR B:317 , PHE B:342 , GLY B:344 , HIS B:345 , GLY B:346 , PHE B:347 , LYS B:348 , MSF B:811 , CL B:814 , HOH B:816 , HOH B:818 , HOH B:824 , HOH B:861 , HOH B:917	BINDING SITE FOR RESIDUE FAD B 400
9	AC9	SOFTWARE	ILE B:50 , ARG B:52 , MET B:245 , TYR B:254 , HIS B:269 , TYR B:317 , GLY B:344 , LYS B:348 , FAD B:400	BINDING SITE FOR RESIDUE MSF B 811

(no "SS Bond" information available for 1EL8)

Asymmetric Unit

No.	Residues
1	Pro A:37	-	Pro A:38
2	Pro B:37	-	Pro B:38

(no "SAP(SNP)/Variant" information available for 1EL8)

(no "PROSITE Motif" information available for 1EL8)

(no "Exon" information available for 1EL8)

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:385
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:385
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
           MSOX_BACB0     2 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 386
               SCOP domains d1el8a1 A:1-217,A:322-385 Sarcosine oxidase                                                                                                                                                                              d1el8a2 A:218-321 Sarcosine oxidase                                                                     d1el8a1 A:1-217,A:322-385 Sarcosine oxidase                      SCOP domains
               CATH domains 1el8A01 A:1-59,A:149-212,A:326-385                         1el8A02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---1el8A01 A:1-59,A:149-212,A:326-385                              1el8A02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----1el8A01 A:1-59,A:149-212,A:326-385                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh...eeee...............eeee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeeehhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee..eeeeeeeeee.hhhhhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh..eeeeee..eeeeee.......eeeee....ee.............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1el8 A   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 385
                                    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       310       320       330       340       350       360       370       380

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:385
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
           MSOX_BACB0     2 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 386
               SCOP domains d1el8b1 B:1-217,B:322-385 Sarcosine oxidase                                                                                                                                                                              d1el8b2 B:218-321 Sarcosine oxidase                                                                     d1el8b1 B:1-217,B:322-385 Sarcosine oxidase                      SCOP domains
               CATH domains 1el8B01 B:1-59,B:149-212,B:326-385                         1el8B02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---1el8B01 B:1-59,B:149-212,B:326-385                              1el8B02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----1el8B01 B:1-59,B:149-212,B:326-385                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh...eeee...............eeee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeeehhhhhhhhhhhhhhh..eee.......eeee..eeee......eeeeeeee.hhhhhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh..eeeeee..eeeeee.......eeeee....ee.............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1el8 B   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 385
                                    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       310       320       330       340       350       360       370       380

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: 2-Layer Sandwich (8480)

Topology: D-Amino Acid Oxidase; Chain A, domain 2 (80)

Homologous Superfamily: D-Amino Acid Oxidase, subunit A, domain 2 (80)

B-0618 (Bacillus sp) (11)

1a	1el8A02	A:60-145,A:213-321
1b	1el8B02	B:60-145,B:213-321

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

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

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

B-0618 (Bacillus sp) (11)

2a	1el8A01	A:1-59,A:149-212,A:326-385
2b	1el8B01	B:1-59,B:149-212,B:326-385

(no "Pfam Domain" information available for 1EL8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MSOX_BACB0 | P40859)

molecular function
	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:0008115	sarcosine oxidase activity	Catalysis of the reaction: H(2)O + O(2) + sarcosine = formaldehyde + glycine + H(2)O(2).
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.
	GO:0046653	tetrahydrofolate metabolic process	The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ 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 ]

	Cis Peptide Bonds
		Pro A:37 - Pro A:38	[ RasMol ]
		Pro B:37 - Pro B:38	[ 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
	1el8
		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
	MSOX_BACB0 \| P40859
		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)
	1.5.3.1
		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
	MSOX_BACB0 \| P40859
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1b3m	MONOMERIC SARCOSINE OXIDASE: STRUCTURE OF A COVALENTLY FLAVINYLATED AMINE OXIDIZING ENZYME
1el5	MONOMERIC SARCOSINE OXIDASE WITH DIMETHYLGLYCINE
1el7	MONOMERIC SARCOSINE OXIDASE WITH [METHYLTELLURO]ACETATE
1el9	MONOMERIC SARCOSINE OXIDASE WITH [METHYLTHIO]ACETATE
1eli	MONOMERIC SARCOSINE OXIDASE WITH PYRROLE-2-CARBOXYLATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

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 (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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