Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5EA2

Crystal Structure of Holo NAD(P)H dehydrogenase, quinone 1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000209	biological_process	protein polyubiquitination
A	0002931	biological_process	response to ischemia
A	0003723	molecular_function	RNA binding
A	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
A	0004128	molecular_function	cytochrome-b5 reductase activity, acting on NAD(P)H
A	0004784	molecular_function	superoxide dismutase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006116	biological_process	NADH oxidation
A	0006743	biological_process	ubiquinone metabolic process
A	0006801	biological_process	superoxide metabolic process
A	0006805	biological_process	xenobiotic metabolic process
A	0006809	biological_process	nitric oxide biosynthetic process
A	0006979	biological_process	response to oxidative stress
A	0007271	biological_process	synaptic transmission, cholinergic
A	0007584	biological_process	response to nutrient
A	0008753	molecular_function	NADPH dehydrogenase (quinone) activity
A	0009410	biological_process	response to xenobiotic stimulus
A	0009636	biological_process	response to toxic substance
A	0009725	biological_process	response to hormone
A	0009743	biological_process	response to carbohydrate
A	0010033	biological_process	obsolete response to organic substance
A	0014070	biological_process	response to organic cyclic compound
A	0014075	biological_process	response to amine
A	0016491	molecular_function	oxidoreductase activity
A	0019430	biological_process	removal of superoxide radicals
A	0030163	biological_process	protein catabolic process
A	0030425	cellular_component	dendrite
A	0032355	biological_process	response to estradiol
A	0032496	biological_process	response to lipopolysaccharide
A	0033574	biological_process	response to testosterone
A	0034599	biological_process	cellular response to oxidative stress
A	0042177	biological_process	negative regulation of protein catabolic process
A	0042360	biological_process	vitamin E metabolic process
A	0042373	biological_process	vitamin K metabolic process
A	0042802	molecular_function	identical protein binding
A	0043025	cellular_component	neuronal cell body
A	0043066	biological_process	negative regulation of apoptotic process
A	0043279	biological_process	response to alkaloid
A	0043525	biological_process	positive regulation of neuron apoptotic process
A	0045087	biological_process	innate immune response
A	0045202	cellular_component	synapse
A	0045454	biological_process	cell redox homeostasis
A	0045471	biological_process	response to ethanol
A	0050136	molecular_function	NADH:ubiquinone reductase (non-electrogenic) activity
A	0051602	biological_process	response to electrical stimulus
A	0070301	biological_process	cellular response to hydrogen peroxide
A	0070995	biological_process	NADPH oxidation
A	0071248	biological_process	cellular response to metal ion
A	0110076	biological_process	negative regulation of ferroptosis
A	1901698	biological_process	response to nitrogen compound
A	1904772	biological_process	response to tetrachloromethane
A	1904844	biological_process	response to L-glutamine
A	1904880	biological_process	response to hydrogen sulfide
A	1905395	biological_process	response to flavonoid
C	0000209	biological_process	protein polyubiquitination
C	0002931	biological_process	response to ischemia
C	0003723	molecular_function	RNA binding
C	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
C	0004128	molecular_function	cytochrome-b5 reductase activity, acting on NAD(P)H
C	0004784	molecular_function	superoxide dismutase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006116	biological_process	NADH oxidation
C	0006743	biological_process	ubiquinone metabolic process
C	0006801	biological_process	superoxide metabolic process
C	0006805	biological_process	xenobiotic metabolic process
C	0006809	biological_process	nitric oxide biosynthetic process
C	0006979	biological_process	response to oxidative stress
C	0007271	biological_process	synaptic transmission, cholinergic
C	0007584	biological_process	response to nutrient
C	0008753	molecular_function	NADPH dehydrogenase (quinone) activity
C	0009410	biological_process	response to xenobiotic stimulus
C	0009636	biological_process	response to toxic substance
C	0009725	biological_process	response to hormone
C	0009743	biological_process	response to carbohydrate
C	0010033	biological_process	obsolete response to organic substance
C	0014070	biological_process	response to organic cyclic compound
C	0014075	biological_process	response to amine
C	0016491	molecular_function	oxidoreductase activity
C	0019430	biological_process	removal of superoxide radicals
C	0030163	biological_process	protein catabolic process
C	0030425	cellular_component	dendrite
C	0032355	biological_process	response to estradiol
C	0032496	biological_process	response to lipopolysaccharide
C	0033574	biological_process	response to testosterone
C	0034599	biological_process	cellular response to oxidative stress
C	0042177	biological_process	negative regulation of protein catabolic process
C	0042360	biological_process	vitamin E metabolic process
C	0042373	biological_process	vitamin K metabolic process
C	0042802	molecular_function	identical protein binding
C	0043025	cellular_component	neuronal cell body
C	0043066	biological_process	negative regulation of apoptotic process
C	0043279	biological_process	response to alkaloid
C	0043525	biological_process	positive regulation of neuron apoptotic process
C	0045087	biological_process	innate immune response
C	0045202	cellular_component	synapse
C	0045454	biological_process	cell redox homeostasis
C	0045471	biological_process	response to ethanol
C	0050136	molecular_function	NADH:ubiquinone reductase (non-electrogenic) activity
C	0051602	biological_process	response to electrical stimulus
C	0070301	biological_process	cellular response to hydrogen peroxide
C	0070995	biological_process	NADPH oxidation
C	0071248	biological_process	cellular response to metal ion
C	0110076	biological_process	negative regulation of ferroptosis
C	1901698	biological_process	response to nitrogen compound
C	1904772	biological_process	response to tetrachloromethane
C	1904844	biological_process	response to L-glutamine
C	1904880	biological_process	response to hydrogen sulfide
C	1905395	biological_process	response to flavonoid
E	0000209	biological_process	protein polyubiquitination
E	0002931	biological_process	response to ischemia
E	0003723	molecular_function	RNA binding
E	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
E	0004128	molecular_function	cytochrome-b5 reductase activity, acting on NAD(P)H
E	0004784	molecular_function	superoxide dismutase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006116	biological_process	NADH oxidation
E	0006743	biological_process	ubiquinone metabolic process
E	0006801	biological_process	superoxide metabolic process
E	0006805	biological_process	xenobiotic metabolic process
E	0006809	biological_process	nitric oxide biosynthetic process
E	0006979	biological_process	response to oxidative stress
E	0007271	biological_process	synaptic transmission, cholinergic
E	0007584	biological_process	response to nutrient
E	0008753	molecular_function	NADPH dehydrogenase (quinone) activity
E	0009410	biological_process	response to xenobiotic stimulus
E	0009636	biological_process	response to toxic substance
E	0009725	biological_process	response to hormone
E	0009743	biological_process	response to carbohydrate
E	0010033	biological_process	obsolete response to organic substance
E	0014070	biological_process	response to organic cyclic compound
E	0014075	biological_process	response to amine
E	0016491	molecular_function	oxidoreductase activity
E	0019430	biological_process	removal of superoxide radicals
E	0030163	biological_process	protein catabolic process
E	0030425	cellular_component	dendrite
E	0032355	biological_process	response to estradiol
E	0032496	biological_process	response to lipopolysaccharide
E	0033574	biological_process	response to testosterone
E	0034599	biological_process	cellular response to oxidative stress
E	0042177	biological_process	negative regulation of protein catabolic process
E	0042360	biological_process	vitamin E metabolic process
E	0042373	biological_process	vitamin K metabolic process
E	0042802	molecular_function	identical protein binding
E	0043025	cellular_component	neuronal cell body
E	0043066	biological_process	negative regulation of apoptotic process
E	0043279	biological_process	response to alkaloid
E	0043525	biological_process	positive regulation of neuron apoptotic process
E	0045087	biological_process	innate immune response
E	0045202	cellular_component	synapse
E	0045454	biological_process	cell redox homeostasis
E	0045471	biological_process	response to ethanol
E	0050136	molecular_function	NADH:ubiquinone reductase (non-electrogenic) activity
E	0051602	biological_process	response to electrical stimulus
E	0070301	biological_process	cellular response to hydrogen peroxide
E	0070995	biological_process	NADPH oxidation
E	0071248	biological_process	cellular response to metal ion
E	0110076	biological_process	negative regulation of ferroptosis
E	1901698	biological_process	response to nitrogen compound
E	1904772	biological_process	response to tetrachloromethane
E	1904844	biological_process	response to L-glutamine
E	1904880	biological_process	response to hydrogen sulfide
E	1905395	biological_process	response to flavonoid
G	0000209	biological_process	protein polyubiquitination
G	0002931	biological_process	response to ischemia
G	0003723	molecular_function	RNA binding
G	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
G	0004128	molecular_function	cytochrome-b5 reductase activity, acting on NAD(P)H
G	0004784	molecular_function	superoxide dismutase activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006116	biological_process	NADH oxidation
G	0006743	biological_process	ubiquinone metabolic process
G	0006801	biological_process	superoxide metabolic process
G	0006805	biological_process	xenobiotic metabolic process
G	0006809	biological_process	nitric oxide biosynthetic process
G	0006979	biological_process	response to oxidative stress
G	0007271	biological_process	synaptic transmission, cholinergic
G	0007584	biological_process	response to nutrient
G	0008753	molecular_function	NADPH dehydrogenase (quinone) activity
G	0009410	biological_process	response to xenobiotic stimulus
G	0009636	biological_process	response to toxic substance
G	0009725	biological_process	response to hormone
G	0009743	biological_process	response to carbohydrate
G	0010033	biological_process	obsolete response to organic substance
G	0014070	biological_process	response to organic cyclic compound
G	0014075	biological_process	response to amine
G	0016491	molecular_function	oxidoreductase activity
G	0019430	biological_process	removal of superoxide radicals
G	0030163	biological_process	protein catabolic process
G	0030425	cellular_component	dendrite
G	0032355	biological_process	response to estradiol
G	0032496	biological_process	response to lipopolysaccharide
G	0033574	biological_process	response to testosterone
G	0034599	biological_process	cellular response to oxidative stress
G	0042177	biological_process	negative regulation of protein catabolic process
G	0042360	biological_process	vitamin E metabolic process
G	0042373	biological_process	vitamin K metabolic process
G	0042802	molecular_function	identical protein binding
G	0043025	cellular_component	neuronal cell body
G	0043066	biological_process	negative regulation of apoptotic process
G	0043279	biological_process	response to alkaloid
G	0043525	biological_process	positive regulation of neuron apoptotic process
G	0045087	biological_process	innate immune response
G	0045202	cellular_component	synapse
G	0045454	biological_process	cell redox homeostasis
G	0045471	biological_process	response to ethanol
G	0050136	molecular_function	NADH:ubiquinone reductase (non-electrogenic) activity
G	0051602	biological_process	response to electrical stimulus
G	0070301	biological_process	cellular response to hydrogen peroxide
G	0070995	biological_process	NADPH oxidation
G	0071248	biological_process	cellular response to metal ion
G	0110076	biological_process	negative regulation of ferroptosis
G	1901698	biological_process	response to nitrogen compound
G	1904772	biological_process	response to tetrachloromethane
G	1904844	biological_process	response to L-glutamine
G	1904880	biological_process	response to hydrogen sulfide
G	1905395	biological_process	response to flavonoid

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	binding site for residue FAD A 301

Chain	Residue
A	HIS11
A	TRP105
A	PHE106
A	THR147
A	THR148
A	GLY149
A	GLY150
A	TYR155
A	ILE192
A	ARG200
A	LEU204
A	THR15
A	HOH467
A	HOH480
C	GLN66
C	HOH484
A	SER16
A	PHE17
A	ASN18
A	ALA20
A	PRO102
A	LEU103
A	GLN104

site_id	AC2
Number of Residues	28
Details	binding site for residue FAD C 301

Chain	Residue
A	GLN66
A	HOH425
C	HIS11
C	THR15
C	SER16
C	PHE17
C	ASN18
C	ALA20
C	PRO102
C	LEU103
C	GLN104
C	TRP105
C	PHE106
C	THR147
C	THR148
C	GLY149
C	GLY150
C	TYR155
C	ILE192
C	ARG200
C	LEU204
C	HOH426
C	HOH445
C	HOH450
C	HOH460
C	HOH482
C	HOH493
C	HOH517

site_id	AC3
Number of Residues	26
Details	binding site for residue FAD E 301

Chain	Residue
E	HIS11
E	THR15
E	SER16
E	PHE17
E	ASN18
E	ALA20
E	PRO102
E	LEU103
E	GLN104
E	TRP105
E	PHE106
E	THR147
E	THR148
E	GLY149
E	GLY150
E	TYR155
E	ILE192
E	ARG200
E	LEU204
E	HOH420
E	HOH451
E	HOH461
E	HOH469
E	HOH494
G	GLN66
G	HOH414

site_id	AC4
Number of Residues	25
Details	binding site for residue FAD G 301

Chain	Residue
G	HOH495
G	HOH535
G	HOH540
E	GLN66
G	HIS11
G	THR15
G	SER16
G	PHE17
G	ASN18
G	ALA20
G	PRO102
G	LEU103
G	GLN104
G	TRP105
G	PHE106
G	THR147
G	THR148
G	GLY149
G	GLY150
G	TYR155
G	ILE192
G	ARG200
G	LEU204
G	HOH404
G	HOH481

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	28
Details	BINDING: BINDING => ECO:0000269\|PubMed:10543876, ECO:0000269\|PubMed:10706635, ECO:0000269\|PubMed:11735396

Chain	Residue	Details
A	HIS11
C	GLN66
C	LEU103
C	THR147
C	TYR155
C	ARG200
E	HIS11
E	PHE17
E	GLN66
E	LEU103
E	THR147
A	PHE17
E	TYR155
E	ARG200
G	HIS11
G	PHE17
G	GLN66
G	LEU103
G	THR147
G	TYR155
G	ARG200
A	GLN66
A	LEU103
A	THR147
A	TYR155
A	ARG200
C	HIS11
C	PHE17

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING:

Chain	Residue	Details
A	ALA125
C	ALA125
E	ALA125
G	ALA125

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER81
C	SER81
E	SER81
G	SER81

site_id	SWS_FT_FI4
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS249
G	LYS249
G	LYS250
A	LYS250
C	LYS249
C	LYS250
E	LYS249
E	LYS250

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	3
Details	M-CSA 3

Chain	Residue	Details
A	GLY149	electrostatic stabiliser, hydrogen bond donor
A	TYR155	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	HIS161	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay

site_id	MCSA2
Number of Residues	3
Details	M-CSA 3

Chain	Residue	Details
C	GLY149	electrostatic stabiliser, hydrogen bond donor
C	TYR155	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
C	HIS161	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay

site_id	MCSA3
Number of Residues	3
Details	M-CSA 3

Chain	Residue	Details
E	GLY149	electrostatic stabiliser, hydrogen bond donor
E	TYR155	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
E	HIS161	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay

site_id	MCSA4
Number of Residues	3
Details	M-CSA 3

Chain	Residue	Details
G	GLY149	electrostatic stabiliser, hydrogen bond donor
G	TYR155	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
G	HIS161	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)