1L5P - 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)

Title :   CRYSTAL STRUCTURE OF TRICHOMONAS VAGINALIS FERREDOXIN

Authors :   C. R. Crossnoe, J. P. Germanas, P. Le Magueres, G. Mustata, K. L. Krause

Date :   07 Mar 02 (Deposition) - 21 Aug 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   [2Fe-2S] Cluster, Electron Transfer, Iron-Sulfur Protein, Metalloprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. R. Crossnoe, J. P. Germanas, P. Lemagueres, G. Mustata, K. L. Krause
The Crystal Structure Of Trichomonas Vaginalis Ferredoxin Provides Insight Into Metronidazole Activation.
J. Mol. Biol. V. 318 503 2002
PubMed-ID: 12051855 | Reference-DOI: 10.1016/S0022-2836(02)00051-7
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PET-3A-TVFD
	Organism Scientific	:	TRICHOMONAS VAGINALIS
	Organism Taxid	:	5722

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:23 , CYS A:38 , GLY A:40 , LYS A:42 , ALA A:43 , CYS A:44 , GLY A:45 , CYS A:47 , CYS A:78	BINDING SITE FOR RESIDUE FES A 94
2	AC2	SOFTWARE	PHE B:23 , THR B:37 , CYS B:38 , GLY B:40 , LYS B:42 , ALA B:43 , CYS B:44 , GLY B:45 , CYS B:47 , CYS B:78	BINDING SITE FOR RESIDUE FES B 94
3	AC3	SOFTWARE	PHE C:23 , CYS C:38 , GLY C:40 , LYS C:42 , ALA C:43 , CYS C:44 , GLY C:45 , CYS C:47 , CYS C:78	BINDING SITE FOR RESIDUE FES C 94

(no "SS Bond" information available for 1L5P)

(no "Cis Peptide Bond" information available for 1L5P)

(no "SAP(SNP)/Variant" information available for 1L5P)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_TRIVA	9-100	3	A:1-93 B:1-93 C:1-93

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_TRIVA	9-100	1	A:1-93 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_TRIVA	9-100	1	- B:1-93 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER_TRIVA	9-100	1	- - C:1-93

(no "Exon" information available for 1L5P)

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:93
 aligned with FER_TRIVA | P21149 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:93
                                                                                      67                                 
                                                                                    66 |                                 
                                    18        28        38        48        58       |67        77        87        97   
            FER_TRIVA     9 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAA-EDDEKEFLEDQPANARLACAITLSGENDGAVFEL 100
               SCOP domains d1l5pa_ A: 2Fe-2S ferredoxin                                                                  SCOP domains
               CATH domains 1l5pA00 A:1-93  [code=3.10.20.30, no name defined]                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee....eehhhhhhh...................eeeeee......hhhhhhhhh.....eee....eehhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE 2FE2S_FER_2  PDB: A:1-93 UniProt: 9-100                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1l5p A   1 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAAAEDDEKEFLEDQPANARLACAITLSGENDGAVFEL  93
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with FER_TRIVA | P21149 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:93
                                                                                      67                                 
                                                                                    66 |                                 
                                    18        28        38        48        58       |67        77        87        97   
            FER_TRIVA     9 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAA-EDDEKEFLEDQPANARLACAITLSGENDGAVFEL 100
               SCOP domains d1l5pb_ B: 2Fe-2S ferredoxin                                                                  SCOP domains
               CATH domains 1l5pB00 B:1-93  [code=3.10.20.30, no name defined]                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee....eehhhhhhh...................eeeeee......hhhhhhhh......eee....eehhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE 2FE2S_FER_2  PDB: B:1-93 UniProt: 9-100                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1l5p B   1 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAAAEDDEKEFLEDQPANARLACAITLSGENDGAVFEL  93
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with FER_TRIVA | P21149 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:93
                                                                                      67                                 
                                                                                    66 |                                 
                                    18        28        38        48        58       |67        77        87        97   
            FER_TRIVA     9 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAA-EDDEKEFLEDQPANARLACAITLSGENDGAVFEL 100
               SCOP domains d1l5pc_ C: 2Fe-2S ferredoxin                                                                  SCOP domains
               CATH domains 1l5pC00 C:1-93  [code=3.10.20.30, no name defined]                                            CATH domains
           Pfam domains (1) -----Fer2-1l5pC01 C:6-83                                                           ---------- Pfam domains (1)
           Pfam domains (2) -----Fer2-1l5pC02 C:6-83                                                           ---------- Pfam domains (2)
           Pfam domains (3) -----Fer2-1l5pC03 C:6-83                                                           ---------- Pfam domains (3)
         Sec.struct. author .eeeeee..eeeeee....eehhhhhhh...................eeeeee......hhhhhhhh......eee....eehhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE 2FE2S_FER_2  PDB: C:1-93 UniProt: 9-100                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1l5p C   1 GTITAVKGGVKKQLKFEDDQTLFTVLTEAGLMSADDTCQGNKACGKCICKHVSGKVAAAEDDEKEFLEDQPANARLACAITLSGENDGAVFEL  93
                                    10        20        30        40        50        60        70        80        90

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) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: 2Fe-2S ferredoxin-like (174)

Family: 2Fe-2S ferredoxin-related (74)

Protein domain: 2Fe-2S ferredoxin (54)

Trichomonas vaginalis [TaxId: 5722] (1)

1a	d1l5pa_	A:
1b	d1l5pb_	B:
1c	d1l5pc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Trichomonas vaginalis. Organism_taxid: 5722. (1)

1a	1l5pA00	A:1-93
1b	1l5pB00	B:1-93
1c	1l5pC00	C:1-93

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Fer2 (69)

Family: Fer2 (60)

Trichomonas vaginalis (1)

1a	Fer2-1l5pC01	C:6-83
1b	Fer2-1l5pC02	C:6-83
1c	Fer2-1l5pC03	C:6-83

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (FER_TRIVA | P21149)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.
cellular component
	GO:0042566	hydrogenosome	A spherical, membrane-bounded organelle found in some anaerobic protozoa, which participates in ATP and molecular hydrogen formation.

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
		FES	[ 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 1l5p)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 ](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
	1l5p
		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
	FER_TRIVA \| P21149
		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
	FER_TRIVA \| P21149
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1L5P)

(no "Related Entries Specified in the PDB File" available for 1L5P)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

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