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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE STRUCTURE OF THE OPEN CONFORMATION OF A FLAVOCYTOCHROME C3 FUMARATE REDUCTASE

Authors :   V. Bamford, P. S. Dobbin, D. J. Richardson, A. M. Hemmings

Date :   04 Nov 99 (Deposition) - 02 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,D

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

Reference :   V. Bamford, P. S. Dobbin, D. J. Richardson, A. M. Hemmings
Open Conformation Of A Flavocytochrome C3 Fumarate Reductase.
Nat. Struct. Biol. V. 6 1104 1999
PubMed-ID: 10581549 | Reference-DOI: 10.1038/70039

Molecule 1 - FLAVOCYTOCHROME C3 FUMARATE REDUCTASE
	Chains	:	A, D
	EC Number	:	1.3.99.1
	Organism Scientific	:	SHEWANELLA FRIGIDIMARINA
	Organism Taxid	:	56812
	Strain	:	NCIMB400

		1	2
Asymmetric/Biological Unit	:	A	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	HEM	8	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:53 , ASP A:54 , SER A:58 , HIS A:59 , LEU A:60 , CYS A:79 , CYS A:82 , HIS A:83 , PHE A:85 , ILE A:162 , ASN A:333 , ILE A:369 , LEU A:433 , HEM A:602 , HOH A:2164 , HOH A:2348 , HOH A:2349 , HOH A:2350 , HOH A:2351 , HOH A:2352	BINDING SITE FOR RESIDUE HEM A 601
02	AC2	SOFTWARE	HIS A:40 , TYR A:43 , LEU A:46 , PRO A:55 , HIS A:56 , CYS A:65 , CYS A:68 , HIS A:69 , LYS A:88 , MET A:90 , HEM A:601 , HEM A:603	BINDING SITE FOR RESIDUE HEM A 602
03	AC3	SOFTWARE	MET A:5 , HIS A:9 , SER A:17 , GLN A:35 , CYS A:36 , CYS A:39 , HIS A:40 , HIS A:69 , PRO A:91 , ASP A:227 , HEM A:602 , HEM A:604 , HOH A:2354 , HOH A:2355	BINDING SITE FOR RESIDUE HEM A 603
04	AC4	SOFTWARE	GLY A:6 , HIS A:9 , CYS A:15 , CYS A:18 , HIS A:19 , GLU A:29 , THR A:66 , LYS A:70 , GLY A:71 , HIS A:72 , HIS A:293 , VAL A:467 , ALA A:468 , SER A:469 , GLY A:470 , HEM A:603 , HOH A:2072 , HOH A:2356	BINDING SITE FOR RESIDUE HEM A 604
05	AC5	SOFTWARE	VAL A:127 , GLY A:128 , GLY A:130 , SER A:131 , ALA A:132 , ASP A:151 , LYS A:152 , GLY A:157 , GLY A:158 , ASN A:159 , SER A:160 , SER A:163 , ALA A:164 , GLY A:165 , GLY A:166 , SER A:271 , ARG A:272 , VAL A:273 , ALA A:307 , THR A:308 , GLY A:309 , SER A:331 , ASN A:332 , THR A:335 , ASP A:339 , HIS A:499 , HIS A:500 , GLY A:528 , GLU A:529 , ARG A:539 , GLY A:542 , ASN A:543 , ALA A:544 , ILE A:545 , THR A:548 , HOH A:2110 , HOH A:2189 , HOH A:2191 , HOH A:2216 , HOH A:2339 , HOH A:2357 , HOH A:2358	BINDING SITE FOR RESIDUE FAD A 605
06	AC6	SOFTWARE	ASP D:54 , SER D:58 , HIS D:59 , LEU D:60 , CYS D:79 , CYS D:82 , HIS D:83 , PHE D:85 , ILE D:162 , ASN D:333 , ILE D:369 , LEU D:433 , HEM D:602	BINDING SITE FOR RESIDUE HEM D 601
07	AC7	SOFTWARE	HIS D:40 , TYR D:43 , LEU D:46 , PRO D:55 , HIS D:56 , CYS D:65 , CYS D:68 , HIS D:69 , PHE D:77 , LYS D:88 , MET D:90 , LYS D:193 , HEM D:601 , HEM D:603	BINDING SITE FOR RESIDUE HEM D 602
08	AC8	SOFTWARE	MET D:5 , HIS D:9 , SER D:17 , CYS D:36 , CYS D:39 , HIS D:40 , HIS D:69 , PRO D:91 , PHE D:92 , LYS D:193 , HEM D:602	BINDING SITE FOR RESIDUE HEM D 603
09	AC9	SOFTWARE	MET D:5 , GLY D:6 , HIS D:9 , CYS D:15 , CYS D:18 , HIS D:19 , ILE D:23 , VAL D:25 , THR D:66 , LYS D:70 , GLY D:71 , HIS D:72 , GLU D:73 , HIS D:293 , HOH D:2146	BINDING SITE FOR RESIDUE HEM D 604
10	BC1	SOFTWARE	VAL D:127 , GLY D:128 , GLY D:130 , SER D:131 , ALA D:132 , ASP D:151 , LYS D:152 , GLY D:157 , GLY D:158 , ASN D:159 , SER D:160 , SER D:163 , ALA D:164 , GLY D:165 , SER D:271 , ARG D:272 , VAL D:273 , ALA D:307 , THR D:308 , GLY D:309 , SER D:331 , ASN D:332 , THR D:335 , ASP D:339 , HIS D:499 , HIS D:500 , GLY D:528 , GLU D:529 , ARG D:539 , GLY D:542 , ASN D:543 , ALA D:544 , ILE D:545 , THR D:548 , HOH D:2132 , HOH D:2134 , HOH D:2147 , HOH D:2148 , HOH D:2149	BINDING SITE FOR RESIDUE FAD D 605

(no "SS Bond" information available for 1QO8)

(no "Cis Peptide Bond" information available for 1QO8)

(no "SAP(SNP)/Variant" information available for 1QO8)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	FRD2_SHEFN	32-110	2	A:10-88 D:10-88

(no "Exon" information available for 1QO8)

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:564
 aligned with FRD2_SHEFN | Q9Z4P0 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:564
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583    
           FRD2_SHEFN    24 TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVFGRIAGDNAAKHALD 587
               SCOP domains d1qo8a1 A:2-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain               d1qo8a2 A:103-359,A:506-565 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                                  d1qo8a3 A:360-505 Flavocytochrome c3 (respiratory fumarate reductase)                                                                             d1qo8a2 A:103-359,A:506-565                                  SCOP domains
               CATH domains 1qo8A02 A:2-97 Flavocytochrome C3; Chain A                                                      ---1qo8A03 A:101-354,A:501-563  [code=3.50.50.60, no name defined]                                                                                                                                                                                               -----1qo8A01 A:360-497 Flavocytochrome C3; Chain A, domain 1                                                                                   ---1qo8A03 A:101-354,A:501-563  [code=3.50.50.60, no name defined]-- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh................hhhhh........hhhhhh.......................hhhhhhhhhhh...eee.eeee..hhhhhhhhhhhhhhh..eeee........hhhhh........hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh.......eeeeeee........eeeeee...eeeeeee.eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh..........eee............hhhhhh..eee............hhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhh...eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh..................eeeeee..eeee.......................eee...............hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------MULTIHEME_CYTC  PDB: A:10-88 UniProt: 32-110                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qo8 A   2 TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVFGRIAGDNAAKHALD 565
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561

Chain D from PDB  Type:PROTEIN  Length:564
 aligned with FRD2_SHEFN | Q9Z4P0 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:564
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583    
           FRD2_SHEFN    24 TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVFGRIAGDNAAKHALD 587
               SCOP domains d1qo8d1 D:2-102 Flavocytochrome c3 (respiratory fumarate reductase), N-terminal domain               d1qo8d2 D:103-359,D:506-565 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                                  d1qo8d3 D:360-505 Flavocytochrome c3 (respiratory fumarate reductase)                                                                             d1qo8d2 D:103-359,D:506-565                                  SCOP domains
               CATH domains 1qo8D02 D:2-100 Flavocytochrome C3; Chain A                                                        ---1qo8D03 D:104-354,D:501-563  [code=3.50.50.60, no name defined]                                                                                                                                                                                            -----1qo8D01 D:360-497 Flavocytochrome C3; Chain A, domain 1                                                                                   ---1qo8D03 D:104-354,D:501-563  [code=3.50.50.60, no name defined]-- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------FAD_binding_2-1qo8D01 D:123-545                                                                                                                                                                                                                                                                                                                                                                                                        -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------FAD_binding_2-1qo8D02 D:123-545                                                                                                                                                                                                                                                                                                                                                                                                        -------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh................hhhhhhhhhhhhhhhhhhh................hhhhh........hhhhhh.......................hhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh...eeee........hhhhh........hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh.......eeeeeee........eeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh.........eeee...........hhhhhhhh.eee............hhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhh...eee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..................eeeeee..eeeee......................eee.hhh...........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------MULTIHEME_CYTC  PDB: D:10-88 UniProt: 32-110                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qo8 D   2 TPDMGSFHADMGSCQSCHAKPIKVTDSETHENAQCKSCHGEYAELANDKLQFDPHNSHLGDINCTSCHKGHEEPKFYCNECHSFDIKPMPFSDAKKKKSWDDGWDQDKIQKAIAAGPSETTQVLVVGAGSAGFNASLAAKKAGANVILVDKAPFSGGNSMISAGGMNAVGTKQQTAHGVEDKVEWFIEDAMKGGRQQNDIKLVTILAEQSADGVQWLESLGANLDDLKRSGGARVDRTHRPHGGKSSGPEIIDTLRKAAKEQGIDTRLNSRVVKLVVNDDHSVVGAVVHGKHTGYYMIGAKSVVLATGGYGMNKEMIAYYRPTMKDMTSSNNITATGDGVLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKDGNRFISELTTRDKASDAILKQPGQFAWIIFDNQLYKKAKMVRGYDHLEMLYKGDTVEQLAKSTGMKVADLAKTVSDYNGYVASGKDTAFGRADMPLNMTQSPYYAVKVAPGIHHTMGGVAINTTASVLDLQSKPIDGLFAAGEVTGGVHGYNRLGGNAIADTVVFGRIAGDNAAKHALD 565
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561

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/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: FAD_binding_2 (21)

Shewanella frigidimarina (strain NCIMB 400) (1)

1a	FAD_binding_2-1qo8D01	D:123-545
1b	FAD_binding_2-1qo8D02	D:123-545

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,D (FRD2_SHEFN | Q9Z4P0)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0000104	succinate dehydrogenase activity	Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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Ligands, Modified Residues, Ions (2, 10)

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