1EFP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ELECTRON TRANSFER FLAVOPROTEIN (ETF) FROM PARACOCCUS DENITRIFICANS

Authors :   D. L. Roberts, D. Salazar, J. P. Fulmer, F. E. Frerman, J. J. -P. Kim

Date :   18 Dec 98 (Deposition) - 09 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Electron Transport, Flavoprotein, Glutaric Acidemia Type Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. L. Roberts, D. Salazar, J. P. Fulmer, F. E. Frerman, J. J. Kim
Crystal Structure Of Paracoccus Denitrificans Electron Transfer Flavoprotein: Structural And Electrostatic Analysis Of A Conserved Flavin Binding Domain.
Biochemistry V. 38 1977 1999
PubMed-ID: 10026281 | Reference-DOI: 10.1021/BI9820917
(for further references see the PDB file header)

Molecule 1 - PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BLUESCRIPT
	Expression System Strain	:	DH5 ALPHA
	Expression System Taxid	:	562
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Other Details	:	FAD AND AMP COFACTORS ARE NONCOVALENTLY BOUND
	Synonym	:	ETF

Molecule 2 - PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN)
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BLUESCRIPT
	Expression System Strain	:	DH5 ALPHA
	Expression System Taxid	:	562
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Other Details	:	FAD AND AMP COFACTORS ARE NONCOVALENTLY BOUND
	Synonym	:	ETF

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:200 , ARG A:201 , GLY A:202 , SER A:226 , ARG A:227 , ALA A:228 , GLN A:240 , VAL A:241 , GLY A:242 , GLN A:243 , THR A:244 , GLY A:245 , GLY A:257 , ILE A:258 , SER A:259 , ALA A:261 , GLN A:263 , HIS A:264 , ASN A:278 , LYS A:279 , ASP A:280 , GLY A:295 , ASP A:296 , LEU A:297 , HOH A:608 , HOH A:614 , TYR B:13 , PHE B:38 , LEU B:182	BINDING SITE FOR RESIDUE FAD A 399
2	AC2	SOFTWARE	PRO B:6 , VAL B:7 , ASN B:36 , ASP B:39 , ILE B:63 , ALA B:119 , GLY B:120 , GLN B:122 , ALA B:123 , ASN B:126 , MET B:128 , ASN B:129 , ALA B:130 , THR B:131	BINDING SITE FOR RESIDUE AMP A 400
3	AC3	SOFTWARE	HOH B:639 , GLY C:200 , ARG C:201 , GLY C:202 , SER C:226 , ARG C:227 , ALA C:228 , GLN C:240 , VAL C:241 , GLY C:242 , GLN C:243 , THR C:244 , GLY C:257 , ILE C:258 , SER C:259 , ALA C:261 , GLN C:263 , HIS C:264 , ASN C:278 , LYS C:279 , ASP C:280 , GLY C:295 , ASP C:296 , LEU C:297 , PHE C:298 , HOH C:609 , TYR D:13	BINDING SITE FOR RESIDUE FAD C 399
4	AC4	SOFTWARE	PRO D:6 , VAL D:7 , ASN D:36 , ASP D:39 , ILE D:63 , ALA D:119 , GLY D:120 , GLN D:122 , ALA D:123 , ASN D:126 , MET D:128 , ASN D:129 , ALA D:130 , THR D:131 , HOH D:606	BINDING SITE FOR RESIDUE AMP C 400

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_PARDE	159-179	2	B:159-179 D:159-179
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_PARDE	252-278	2	A:252-278 C:252-278

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_PARDE	159-179	1	B:159-179 -
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_PARDE	252-278	1	A:252-278 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_PARDE	159-179	1	- D:159-179
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_PARDE	252-278	1	- C:252-278

(no "Exon" information available for 1EFP)

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:307
 aligned with ETFA_PARDE | P38974 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:307
                                    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       
           ETFA_PARDE     2 AVLLLGEVTNGALNRDATAKAVAAVKALGDVTVLCAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAPATTDAKNVMPRVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAESDRPELTSARRVVSGGRGLGSKESFAIIEELADKLGAAVGASRAAVDSGYAPNDWQVGQTGKVVAPELYVAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQIADYGLVGDLFSVVPELTGKL 308
               SCOP domains d1efpa1 A:2-184 Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain                                                                                         d1efpa2 A:185-308 C-terminal domain of the electron transfer flavoprotein alpha subunit                                      SCOP domains
               CATH domains 1efpA02 A:2-182 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                1efpA01 A:183-308 TPP-binding domain                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........hhhhhhhhhhhhhh..eeeeeee...hhhhhhhh....eeeeeeee.hhh....hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh........eeee....eeeeeehhh.eeeeee.....eeeee.hhh...........................................eeeee.hhh....hhhhhhhhhhhh..eeee.hhhhh.....hhh............eeeee.....hhhhhh.....eeeeee.....hhhh...eeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: A:252-278  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efp A   2 AVLLLGEVTNGALNRDATAKAVAAVKALGDVTVLCAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAPATTDAKNVMPRVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAESDRPELTSARRVVSGGRGLGSKESFAIIEELADKLGAAVGASRAAVDSGYAPNDWQVGQTGKVVAPELYVAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQIADYGLVGDLFSVVPELTGKL 308
                                    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

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with ETFB_PARDE | P38975 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           ETFB_PARDE     1 MKVLVPVKRLIDYNVKARVKSDGSGVDLANVKMSMNPFDEIAVEEAIRLKEKGQAEEIIAVSIGVKQAAETLRTALAMGADRAILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDNDMNATGQMLAAILGWAQATFASKVEIEGAKAKVTREVDGGLQTIAVSLPAVVTADLRLNEPRYASLPNIMKAKKKPLDEKTAADYGVDVAPRLEVVSVREPEGRKAGIKVGSVDELVGKL 246
               SCOP domains d1efpb_ B: Small, beta subunit of electron transfer flavoprotein ETFP                                                                                                                                                                                  SCOP domains
               CATH domains 1efpB00 B:1-246 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eee.....................eee.hhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhh..eee..eeeeee...eeeeeeee..eeeeeeee..eeeee...........hhhhhhhhh..eeeeehhhh...........................hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA             ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1efp B   1 MKVLVPVKRLIDYNVKARVKSDGSGVDLANVKMSMNPFDEIAVEEAIRLKEKGQAEEIIAVSIGVKQAAETLRTALAMGADRAILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDNDMNATGQMLAAILGWAQATFASKVEIEGAKAKVTREVDGGLQTIAVSLPAVVTADLRLNEPRYASLPNIMKAKKKPLDEKTAADYGVDVAPRLEVVSVREPEGRKAGIKVGSVDELVGKL 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain C from PDB  Type:PROTEIN  Length:307
 aligned with ETFA_PARDE | P38974 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:307
                                    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       
           ETFA_PARDE     2 AVLLLGEVTNGALNRDATAKAVAAVKALGDVTVLCAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAPATTDAKNVMPRVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAESDRPELTSARRVVSGGRGLGSKESFAIIEELADKLGAAVGASRAAVDSGYAPNDWQVGQTGKVVAPELYVAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQIADYGLVGDLFSVVPELTGKL 308
               SCOP domains d1efpc1 C:2-184 Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain                                                                                         d1efpc2 C:185-308 C-terminal domain of the electron transfer flavoprotein alpha subunit                                      SCOP domains
               CATH domains 1efpC02 C:2-182 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                1efpC01 C:183-308 TPP-binding domain                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........hhhhhhhhhhhhhh..eeeeeee...hhhhhhhh....eeeeeeee.hhh....hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh........eeee....eeeeeehhh.eeeeee.....eeeee.hhh............eee.......................hhh..eeeee.hhh....hhhhhhhhhhhh..eeee.hhhhh.....hhh............eeeee.....hhhhhh.....eeeeee.....hhhh...eeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: C:252-278  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efp C   2 AVLLLGEVTNGALNRDATAKAVAAVKALGDVTVLCAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAPATTDAKNVMPRVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGTAPVTETAAAADPGLSSWVADEVAESDRPELTSARRVVSGGRGLGSKESFAIIEELADKLGAAVGASRAAVDSGYAPNDWQVGQTGKVVAPELYVAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQIADYGLVGDLFSVVPELTGKL 308
                                    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

Chain D from PDB  Type:PROTEIN  Length:246
 aligned with ETFB_PARDE | P38975 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           ETFB_PARDE     1 MKVLVPVKRLIDYNVKARVKSDGSGVDLANVKMSMNPFDEIAVEEAIRLKEKGQAEEIIAVSIGVKQAAETLRTALAMGADRAILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDNDMNATGQMLAAILGWAQATFASKVEIEGAKAKVTREVDGGLQTIAVSLPAVVTADLRLNEPRYASLPNIMKAKKKPLDEKTAADYGVDVAPRLEVVSVREPEGRKAGIKVGSVDELVGKL 246
               SCOP domains d1efpd_ D: Small, beta subunit of electron transfer flavoprotein ETFP                                                                                                                                                                                  SCOP domains
               CATH domains 1efpD00 D:1-246 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eee.....................eee.hhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhh....eeeee..........hhhhhhhhh..eee..eeeeeee..eeeeeeee..eeeeeeee..eeeee...........hhhhhhhhh..eeeeehhhh...........................hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA             ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1efp D   1 MKVLVPVKRLIDYNVKARVKSDGSGVDLANVKMSMNPFDEIAVEEAIRLKEKGQAEEIIAVSIGVKQAAETLRTALAMGADRAILVVAADDVQQDIEPLAVAKILAAVARAEGTELIIAGKQAIDNDMNATGQMLAAILGWAQATFASKVEIEGAKAKVTREVDGGLQTIAVSLPAVVTADLRLNEPRYASLPNIMKAKKKPLDEKTAADYGVDVAPRLEVVSVREPEGRKAGIKVGSVDELVGKL 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Paracoccus denitrificans. Organism_taxid: 266. (1)

1a	1efpA01	A:183-308
1b	1efpC01	C:183-308

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Paracoccus denitrificans. Organism_taxid: 266. (1)

2a	1efpA02	A:2-182
2b	1efpC02	C:2-182
2c	1efpB00	B:1-246
2d	1efpD00	D:1-246

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (ETFA_PARDE | P38974)

molecular function
	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:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
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.

Chain B,D (ETFB_PARDE | P38975)

molecular function
	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
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	Cis Peptide Bonds
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Biological Units
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	1efp
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(no "Entries Sharing at Least One Protein Chain" available for 1EFP)

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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