1FTC - 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)

Title :   Y13C MUTANT OF AZOTOBACTER VINELANDII FDI

Authors :   M. A. Kemper, S. J. Lloyd, G. S. Prasad, C. D. Stout, S. Fawcett, F. A. Armstrong, B. K. Burgess

Date :   08 Jan 97 (Deposition) - 01 Apr 97 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Electron Transport, Iron-Sulfur (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Kemper, C. D. Stout, S. J. Lloyd, G. S. Prasad, S. E. Fawcett, F. A. Armstrong, B. Shen, B. K. Burgess
Y13C Azotobacter Vinelandii Ferredoxin I. A Designed [Fe-S] Ligand Motif Contains A Cysteine Persulfide.
J. Biol. Chem. V. 272 15620 1997
PubMed-ID: 9188450 | Reference-DOI: 10.1074/JBC.272.25.15620
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	AZOTOBACTER VINELANDII
	Expression System Taxid	:	354
	Mutation	:	YES
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Other Details	:	CYS 13 MODIFIED TO A PERSULFIDE, [3FE-4S] AND [4FE-4S] CLUSTERS AS IN NATIVE PROTEIN
	Strain	:	JG100

		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 (3, 6)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	F3S	2	Ligand/Ion	FE3-S4 CLUSTER
3	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:20 , VAL A:22 , CYS A:24 , PHE A:25 , ILE A:34 , CYS A:39 , ILE A:40 , CYS A:42 , ALA A:43 , CYS A:45	BINDING SITE FOR RESIDUE SF4 A 107
2	AC2	SOFTWARE	VAL A:4 , CYS A:8 , LYS A:12 , CSS A:13 , THR A:14 , ASP A:15 , CYS A:16 , LEU A:32 , CYS A:49 , ILE A:54	BINDING SITE FOR RESIDUE F3S A 108
3	AC3	SOFTWARE	PHE B:2 , CYS B:20 , VAL B:22 , CYS B:24 , PHE B:25 , ILE B:34 , CYS B:39 , ILE B:40 , CYS B:42 , ALA B:43 , CYS B:45	BINDING SITE FOR RESIDUE SF4 B 107
4	AC4	SOFTWARE	VAL B:4 , CYS B:8 , CSS B:13 , THR B:14 , ASP B:15 , CYS B:16 , CYS B:49 , ILE B:54	BINDING SITE FOR RESIDUE F3S B 108

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER1_AZOVI	31-60 1-30	2	A:30-59 B:30-59 -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	2	A:39-50 B:39-50

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER1_AZOVI	31-60 1-30	1	A:30-59 - -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	A:39-50 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER1_AZOVI	31-60 1-30	1	- B:30-59 -
2	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER1_AZOVI	40-51	1	- B:39-50

(no "Exon" information available for 1FTC)

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:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1ftca_ A: Ferredoxin                                                                                      SCOP domains
               CATH domains 1ftcA00 A:1-106  [code=3.30.70.20, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh......hhhhh.....eee....eee.........hhhhh.....eeehhh..hhhhhhhhhhhhhhhh.............hhhh.....hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: A:30-59     ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1ftc A   1 AFVVTDNCIKCKcTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 106
                                    10  |     20        30        40        50        60        70        80        90       100      
                                       13-CSS

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1ftcb_ B: Ferredoxin                                                                                      SCOP domains
               CATH domains 1ftcB00 B:1-106  [code=3.30.70.20, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh......hhhhh.....eee....eee.........hhhhh.....eeehhh..hhhhhhhhhhhhhhhh.............hhhh.....hhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: B:30-59     ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1ftc B   1 AFVVTDNCIKCKcTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 106
                                    10  |     20        30        40        50        60        70        80        90       100      
                                       13-CSS

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: Ferredoxin-like (1795)

Superfamily: 4Fe-4S ferredoxins (143)

Family: 7-Fe ferredoxin (40)

Protein domain: Ferredoxin (37)

Azotobacter vinelandii [TaxId: 354] (32)

1a	d1ftca_	A:
1b	d1ftcb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.20, no name defined] (120)

Azotobacter vinelandii. Organism_taxid: 354. Strain: jg100. (2)

1a	1ftcA00	A:1-106
1b	1ftcB00	B:1-106

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (FER1_AZOVI | P00214)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.

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
		CSS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		F3S	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SF4	[ 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 1ftc)

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
	1ftc
		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
	FER1_AZOVI \| P00214
		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
	FER1_AZOVI \| P00214
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

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