2GR0 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FERREDOXIN REDUCTASE, BPHA4 (OXIDIZED FORM, NAD+ COMPLEX)

Authors :   T. Senda, M. Senda

Date :   22 Apr 06 (Deposition) - 22 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

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

Reference :   M. Senda, S. Kishigami, S. Kimura, M. Fukuda, T. Ishida, T. Senda
Molecular Mechanism Of The Redox-Dependent Interaction Between Nadh-Dependent Ferredoxin Reductase And Rieske-Type [2Fe-2S] Ferredoxin
J. Mol. Biol. V. 373 382 2007
PubMed-ID: 17850818 | Reference-DOI: 10.1016/J.JMB.2007.08.002

Molecule 1 - FERREDOXIN REDUCTASE
	Chains	:	A
	EC Number	:	1.18.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PSEUDOMONAS SP. KKS102
	Organism Taxid	:	307
	Synonym	:	FERREDOXIN REDUCTASE BPHA4

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , GLY A:16 , LEU A:17 , ALA A:18 , VAL A:38 , ASP A:40 , GLU A:41 , ARG A:48 , PRO A:49 , SER A:52 , LYS A:53 , VAL A:80 , ALA A:82 , ALA A:108 , THR A:109 , GLY A:110 , ARG A:130 , ILE A:156 , GLY A:272 , ASP A:273 , GLU A:289 , THR A:290 , TRP A:291 , ALA A:294 , TYR A:319 , TRP A:320 , HOH A:1450 , HOH A:1451 , HOH A:1452 , HOH A:1456 , HOH A:1459 , HOH A:1478 , HOH A:1484 , HOH A:1486 , HOH A:1535	BINDING SITE FOR RESIDUE FAD A 1449
2	AC2	SOFTWARE	ARG A:114 , LEU A:116 , VAL A:151 , GLY A:152 , GLY A:153 , GLY A:154 , ILE A:156 , GLU A:175 , THR A:176 , GLN A:177 , SER A:182 , ARG A:183 , GLY A:234 , ILE A:235 , GLY A:236 , HOH A:1536 , HOH A:1646 , HOH A:1673 , HOH A:1684 , HOH A:1685 , HOH A:1696	BINDING SITE FOR RESIDUE ADP A 1001

(no "SS Bond" information available for 2GR0)

Asymmetric Unit

No.	Residues
1	Ala A:8	-	Pro A:9

(no "SAP(SNP)/Variant" information available for 2GR0)

(no "PROSITE Motif" information available for 2GR0)

(no "Exon" information available for 2GR0)

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:401
 aligned with Q52437_PSES1 | Q52437 from UniProtKB/TrEMBL  Length:408

    Alignment length:401
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
         Q52437_PSES1     6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
               SCOP domains d2gr0a1 A:6-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4                                          d2gr0a2 A:116-236 NADH-dependent ferredoxin reductase, BphA4                                                             d2gr0a1 A:6-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4    d2gr0a3 A:309-406 NADH-dependent ferredoxin reductase, BphA4                                       SCOP domains
               CATH domains 2gr0A01 A:6-110,A:239-317  [code=3.50.50.60, no name defined]                                            ---2gr0A02 A:114-236  [code=3.50.50.60, no name defined]                                                                      --2gr0A01 A:6-110,A:239-317  [code=3.50.50.60, no name defined]                  2gr0A03 A:318-406  [code=3.30.390.30, no name defined]                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh..........eeee...eeeee....eeee....eee..eeee...eee..hhhhh.....eee..hhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhh..eeee...eeeee..eeee....eee..eeee...eee.hhhhhhhh......ee...........eee....eeeee....eee...hhhhhhhhhhhhhhhhhh..........eeeeee..eeeeeee.....eeeee.........eeeeeee..eeeeeeee.hhhhhhhhhhhhhh....hhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gr0 A   6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

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: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

Kks102 (Pseudomonas sp) (7)

2gr0A03

A:318-406

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Kks102 (Pseudomonas sp) (7)

2a	2gr0A01	A:6-110,A:239-317
2b	2gr0A02	A:114-236

(no "Pfam Domain" information available for 2GR0)

Asymmetric Unit(hide GO term definitions)

Chain A (Q52437_PSES1 | Q52437)

molecular function
	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.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:8 - Pro A:9	[ RasMol ]

Biological Unit
	Complete Structure
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	2gr0
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	1.18.1.2
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	Q52437_PSES1 \| Q52437	:	1d7y 1f3p 2gqw 2gr1 2gr2 2gr3 2yvf 2yvg 2yvj

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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