3F6R - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   DESULFOVIBRIO DESULFURICANS (ATCC 29577) OXIDIZED FLAVODOXIN

Authors :   M. Guelker, Y. Shamoo

Date :   06 Nov 08 (Deposition) - 09 Jun 09 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Flavodoxin-Like Fold, Fmn Binding, Oxidized, Electron Transport, Flavoprotein, Fmn, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Guelker, L. Stagg, P. Wittung-Stafshede, Y. Shamoo
Pseudosymmetry, High Copy Number And Twinning Complicate The Structure Determination Of Desulfovibrio Desulfuricans (Atcc 29577) Flavodoxin.
Acta Crystallogr. , Sect. D V. 65 523 2009
PubMed-ID: 19465766 | Reference-DOI: 10.1107/S0907444909010075
(for further references see the PDB file header)

Molecule 1 - FLAVODOXIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-24C(+)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FLAVODOXIN
	Mutation	:	YES
	Organism Scientific	:	DESULFOVIBRIO DESULFURICANS
	Organism Taxid	:	876
	Strain	:	ATCC 29577

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:10 , SER A:11 , THR A:12 , GLY A:13 , ASN A:14 , THR A:15 , SER A:58 , ALA A:59 , TRP A:60 , SER A:93 , GLY A:94 , ASP A:95 , TYR A:98 , HIS A:100 , PHE A:101 , CYS A:102 , HOH A:160	BINDING SITE FOR RESIDUE FMN A 149
2	AC2	SOFTWARE	SER B:10 , SER B:11 , THR B:12 , GLY B:13 , ASN B:14 , THR B:15 , ALA B:28 , SER B:58 , ALA B:59 , TRP B:60 , GLY B:61 , SER B:93 , GLY B:94 , ASP B:95 , TYR B:98 , HIS B:100 , PHE B:101 , CYS B:102 , HOH B:151 , HOH B:301	BINDING SITE FOR RESIDUE FMN B 150
3	AC3	SOFTWARE	SER C:10 , SER C:11 , THR C:12 , GLY C:13 , ASN C:14 , THR C:15 , ALA C:28 , SER C:58 , ALA C:59 , TRP C:60 , GLY C:61 , SER C:93 , GLY C:94 , ASP C:95 , TYR C:98 , HIS C:100 , PHE C:101 , CYS C:102 , HOH C:169	BINDING SITE FOR RESIDUE FMN C 151
4	AC4	SOFTWARE	SER D:10 , SER D:11 , THR D:12 , GLY D:13 , ASN D:14 , THR D:15 , ALA D:28 , SER D:58 , ALA D:59 , TRP D:60 , GLY D:61 , SER D:93 , GLY D:94 , ASP D:95 , TYR D:98 , HIS D:100 , PHE D:101 , CYS D:102 , HOH D:153	BINDING SITE FOR RESIDUE FMN D 152

(no "SS Bond" information available for 3F6R)

(no "Cis Peptide Bond" information available for 3F6R)

(no "SAP(SNP)/Variant" information available for 3F6R)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_DESDE	4-145	4	A:4-145 B:4-145 C:4-145 D:4-145
2	FLAVODOXIN	PS00201	Flavodoxin signature.	FLAV_DESDE	6-22	4	A:6-22 B:6-22 C:6-22 D:6-22

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_DESDE	4-145	1	A:4-145 - - -
2	FLAVODOXIN	PS00201	Flavodoxin signature.	FLAV_DESDE	6-22	1	A:6-22 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_DESDE	4-145	1	- B:4-145 - -
2	FLAVODOXIN	PS00201	Flavodoxin signature.	FLAV_DESDE	6-22	1	- B:6-22 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_DESDE	4-145	1	- - C:4-145 -
2	FLAVODOXIN	PS00201	Flavodoxin signature.	FLAV_DESDE	6-22	1	- - C:6-22 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_DESDE	4-145	1	- - - D:4-145
2	FLAVODOXIN	PS00201	Flavodoxin signature.	FLAV_DESDE	6-22	1	- - - D:6-22

(no "Exon" information available for 3F6R)

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:147
 aligned with FLAV_DESDE | P26492 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESDE     2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFNRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
               SCOP domains d3f6ra_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 3f6rA00 A:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhh...eeeeee..............eeeeee.ee.....eehhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: A:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6r A   2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFDRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with FLAV_DESDE | P26492 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESDE     2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFNRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
               SCOP domains d3f6rb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 3f6rB00 B:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhh...eeeeee..............eeeeee.ee.....eehhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhh..ee....eee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: B:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6r B   2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFDRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with FLAV_DESDE | P26492 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESDE     2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFNRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
               SCOP domains d3f6rc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains 3f6rC00 C:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhh...eeeeee.hhh..........eeeeee.ee.....eehhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: C:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6r C   2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFDRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:147
 aligned with FLAV_DESDE | P26492 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           FLAV_DESDE     2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFNRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
               SCOP domains d3f6rd_ D: automated matches                                                                                                                        SCOP domains
               CATH domains 3f6rD00 D:2-148  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhh...eeeeee..............eeeeee.ee.....eehhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FLAVODOXIN_LIKE  PDB: D:4-145 UniProt: 4-145                                                                                                  --- PROSITE (1)
                PROSITE (2) ----FLAVODOXIN       ------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f6r D   2 SKVLIVFGSSTGNTESIAQKLEELIAAGGHEVTLLNAADASAENLADGYDAVLFGCSAWGMEDLEMQDDFLSLFEEFDRIGLAGRKVAAFASGDQEYEHFCGAVPAIEERAKELGATIIAEGLKMEGDASNDPEAVASFAEDVLKQL 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: automated matches (29)

Protein domain: automated matches (29)

Desulfovibrio desulfuricans [TaxId: 876] (3)

1a	d3f6ra_	A:
1b	d3f6rb_	B:
1c	d3f6rc_	C:
1d	d3f6rd_	D:

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=3.40.50.360, no name defined] (150)

Desulfovibrio desulfuricans. Organism_taxid: 876. Strain: atcc 29577. (3)

1a	3f6rA00	A:2-148
1b	3f6rB00	B:2-148
1c	3f6rC00	C:2-148
1d	3f6rD00	D:2-148

(no "Pfam Domain" information available for 3F6R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (FLAV_DESDE | P26492)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
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
		FMN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3f6r)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	3f6r
		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
	FLAV_DESDE \| P26492
		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)
	(no 'Enzyme Classificator' available)
		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
	FLAV_DESDE \| P26492
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	FLAV_DESDE \| P26492	:	3f6s 3f90

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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