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Description

Title :   REPLACEMENT FOR 1FDX 2(4FE4S) FERREDOXIN FROM (NOW) PEPTOSTREPTOCOCCUS ASACCHAROLYTICUS

Authors :   E. T. Adman, L. C. Sieker

Date :   18 Jan 00 (Deposition) - 29 Mar 00 (Release) - 13 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Two 4Fe-4S Clusters, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. T. Adman, L. C. Sieker
The 2[4Fe-4S] Ferredoxins
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - 2[4FE-4S] FERREDOXIN
	Chains	:	A
	Organism Scientific	:	PEPTONIPHILUS ASACCHAROLYTICUS
	Organism Taxid	:	1258
	Other Details	:	FORMERLY CALLED PEPTOCOCCUS AEROGENES

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:8 , ILE A:9 , CYS A:11 , GLY A:12 , CYS A:14 , CYS A:46 , VAL A:48	BINDING SITE FOR RESIDUE SF4 A 56
2	AC2	SOFTWARE	CYS A:18 , CYS A:22 , ILE A:31 , CYS A:36 , ILE A:37 , CYS A:39 , GLY A:40 , CYS A:42	BINDING SITE FOR RESIDUE SF4 A 57

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 4)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	FER_PEPAS	8-19 35-46	2	A:8-19 A:36-47
2	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_PEPAS	26-54 1-22	2	A:27-55 A:1-23

Exons (0, 0)

(no "Exon" information available for 1DUR)

Sequences/Alignments

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:55
 aligned with FER_PEPAS | P00193 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:55
                                                 22                                
                                               21 |                                
                                    10        20| |     29        39        49     
             FER_PEPAS    1 AYVINDSCIACGACKPECPVN-IQQGSIYAIDADSCIDCGSCASVCPVGAPNPED 54
               SCOP domains d1dura_ A: Ferredoxin II                                SCOP domains
               CATH domains 1durA00 A:1-55  [code=3.30.70.20, no name defined]      CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.........hhhhh....ee.....ee........hhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------4FE4S_FER_1 ----------------4FE4S_FER_1 -------- PROSITE (1)
                PROSITE (2) 4FE4S_FER_2  PDB: A:1-2---4FE4S_FER_2  PDB: A:27-55     PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                  1dur A  1 AYVINDSCIACGACKPECPVNCIQEGSIYAIDADSCIDCGSCASVCPVGAPNPED 55
                                    10        20        30        40        50

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological 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: Short-chain ferredoxins (11)

Protein domain: Ferredoxin II (7)

Peptostreptococcus asaccharolyticus [TaxId: 1258] (1)

d1dura_

CATH Domains (1, 1)

Asymmetric/Biological 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)

Peptoniphilus asaccharolyticus. Organism_taxid: 1258. (1)

1durA00

A:1-55

Pfam Domains (0, 0)

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

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FER_PEPAS | P00193)

molecular function
	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: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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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Related Entries Specified in the PDB File

1fdx	CURRENT DEPOSITION IS REPLACEMENT FOR 1FDX