Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3HRD

Crystal structure of nicotinate dehydrogenase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0016491	molecular_function	oxidoreductase activity
A	0046872	molecular_function	metal ion binding
A	0050138	molecular_function	nicotinate dehydrogenase activity
A	1901848	biological_process	nicotinate catabolic process
B	0005506	molecular_function	iron ion binding
B	0016491	molecular_function	oxidoreductase activity
B	0046872	molecular_function	metal ion binding
B	0050138	molecular_function	nicotinate dehydrogenase activity
B	1901848	biological_process	nicotinate catabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0050138	molecular_function	nicotinate dehydrogenase activity
C	0050660	molecular_function	flavin adenine dinucleotide binding
C	0071949	molecular_function	FAD binding
C	1901848	biological_process	nicotinate catabolic process
D	0000166	molecular_function	nucleotide binding
D	0016491	molecular_function	oxidoreductase activity
D	0046872	molecular_function	metal ion binding
D	0050138	molecular_function	nicotinate dehydrogenase activity
D	0051536	molecular_function	iron-sulfur cluster binding
D	0051537	molecular_function	2 iron, 2 sulfur cluster binding
D	1901848	biological_process	nicotinate catabolic process
E	0005506	molecular_function	iron ion binding
E	0016491	molecular_function	oxidoreductase activity
E	0046872	molecular_function	metal ion binding
E	0050138	molecular_function	nicotinate dehydrogenase activity
E	1901848	biological_process	nicotinate catabolic process
F	0005506	molecular_function	iron ion binding
F	0016491	molecular_function	oxidoreductase activity
F	0046872	molecular_function	metal ion binding
F	0050138	molecular_function	nicotinate dehydrogenase activity
F	1901848	biological_process	nicotinate catabolic process
G	0016491	molecular_function	oxidoreductase activity
G	0050138	molecular_function	nicotinate dehydrogenase activity
G	0050660	molecular_function	flavin adenine dinucleotide binding
G	0071949	molecular_function	FAD binding
G	1901848	biological_process	nicotinate catabolic process
H	0000166	molecular_function	nucleotide binding
H	0016491	molecular_function	oxidoreductase activity
H	0046872	molecular_function	metal ion binding
H	0050138	molecular_function	nicotinate dehydrogenase activity
H	0051536	molecular_function	iron-sulfur cluster binding
H	0051537	molecular_function	2 iron, 2 sulfur cluster binding
H	1901848	biological_process	nicotinate catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SE A 922

Chain	Residue
A	PHE239
A	GLY240
A	ALA349
A	PHE350
A	ARG351
B	GLU289
B	MOS920
B	MCN921

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE NO3 A 5658

Chain	Residue
A	HIS279
A	VAL316
A	GLY348
A	ALA349
A	PHE350
A	PHE353
A	GLY354
A	GLN357
A	ARG278

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MG A 426

Chain	Residue
A	THR207
A	ASN209
A	ASP213
A	LYS242
A	LEU243
A	ASP244
A	GLN248
A	HOH448

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 427

Chain	Residue
A	THR306
A	TYR309
A	ALA310
A	SER347

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE MOS B 920

Chain	Residue
A	GLN208
A	GLY240
A	LEU243
A	PHE353
A	SE922
B	THR84
B	SER85
B	ALA86
B	GLU289
B	MCN921

site_id	AC6
Number of Residues	35
Details	BINDING SITE FOR RESIDUE MCN B 921

Chain	Residue
A	GLY237
A	GLY238
A	PHE239
A	ARG351
A	SE922
B	ILE45
B	GLY46
B	GLN47
B	GLY48
B	SER49
B	THR84
B	SER85
B	ALA86
B	SER87
B	ARG88
B	GLN89
B	THR90
B	VAL211
B	THR213
B	ILE215
B	ASN216
B	MET219
B	VAL220
B	GLN223
B	ALA284
B	LYS285
B	GLY286
B	VAL287
B	GLY288
B	GLU289
B	HOH384
B	HOH446
B	MOS920
D	GLN100
D	CYS138

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE NIO B 5661

Chain	Residue
A	TYR312
A	ALA315
A	ARG319
A	PHE353
A	HOH513
B	ASN17
B	THR18
B	LEU20

site_id	AC8
Number of Residues	33
Details	BINDING SITE FOR RESIDUE FAD C 900

Chain	Residue
C	THR117
C	GLY122
C	ASP123
C	ARG160
C	ILE168
C	MET169
C	LYS187
C	ALA195
C	HOH303
C	HOH329
C	HOH359
C	HOH361
C	HOH388
D	GLU44
D	GLY45
D	GLU46
C	ILE29
C	ALA31
C	GLY32
C	GLY33
C	THR34
C	ASP35
C	LEU36
C	ILE38
C	ALA73
C	PHE77
C	VAL100
C	GLY101
C	ILE105
C	THR110
C	GLY113
C	ASN114
C	SER116

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NO3 C 5659

Chain	Residue
C	CYS222
C	ARG265
C	PRO266
C	SER267
C	VAL268
C	LYS271

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FES D 907

Chain	Residue
A	ILE186
D	GLN100
D	CYS101
D	GLY102
D	CYS104
D	CYS136
D	ARG137
D	CYS138

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FES D 908

Chain	Residue
D	GLY41
D	CYS42
D	SER43
D	GLY45
D	GLU46
D	CYS47
D	GLY48
D	CYS50
D	THR60
D	CYS62

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SE E 922

Chain	Residue
E	PHE239
E	GLY240
E	ALA349
E	PHE350
E	ARG351
F	GLU289
F	MOS920
F	MCN921

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE NIO E 5660

Chain	Residue
A	GLU198
E	VAL15
E	GLU19
E	HOH441
E	HOH757
F	VAL70
F	THR71
F	TRP72

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE NO3 E 5662

Chain	Residue
E	ARG278
E	HIS279
E	VAL316
E	GLY348
E	ALA349
E	PHE350
E	GLY354
E	GLN357

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA E 5663

Chain	Residue
E	THR207
E	ASN209
E	ASP213
E	LYS242
E	LEU243
E	ASP244
E	GLN248

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MOS F 920

Chain	Residue
E	GLN208
E	GLY240
E	LEU243
E	SE922
F	THR84
F	SER85
F	ALA86
F	GLU289
F	MCN921

site_id	BC8
Number of Residues	34
Details	BINDING SITE FOR RESIDUE MCN F 921

Chain	Residue
E	GLY238
E	PHE239
E	ARG351
E	SE922
F	ILE45
F	GLY46
F	GLN47
F	GLY48
F	SER49
F	THR84
F	SER85
F	ALA86
F	SER87
F	ARG88
F	GLN89
F	THR90
F	VAL211
F	THR213
F	ILE215
F	ASN216
F	MET219
F	VAL220
F	GLN223
F	ALA284
F	LYS285
F	GLY286
F	VAL287
F	GLY288
F	GLU289
F	HOH333
F	HOH895
F	MOS920
H	GLN100
H	CYS138

site_id	BC9
Number of Residues	29
Details	BINDING SITE FOR RESIDUE FAD G 900

Chain	Residue
G	ILE29
G	ALA31
G	GLY32
G	GLY33
G	THR34
G	ASP35
G	LEU36
G	ILE38
G	ILE53
G	PHE77
G	VAL100
G	GLY101
G	ILE105
G	THR110
G	GLY113
G	ASN114
G	SER116
G	THR117
G	GLY122
G	ASP123
G	ARG160
G	ILE168
G	MET169
G	LYS187
G	ALA195
G	HOH297
H	GLU44
H	GLY45
H	GLU46

site_id	CC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FES H 907

Chain	Residue
E	ILE186
H	GLN100
H	CYS101
H	GLY102
H	CYS104
H	CYS136
H	ARG137
H	CYS138

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FES H 908

Chain	Residue
H	GLY41
H	CYS42
H	SER43
H	GLY45
H	GLU46
H	CYS47
H	GLY48
H	CYS50
H	CYS62

Functional Information from PROSITE/UniProt

site_id	PS00197
Number of Residues	9
Details	2FE2S_FER_1 2Fe-2S ferredoxin-type iron-sulfur binding region signature. CSEGECGAC

Chain	Residue	Details
D	CYS42-CYS50

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	90
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19549881","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P80457","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	356
Details	Domain: {"description":"FAD-binding PCMH-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00718","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	152
Details	Domain: {"description":"2Fe-2S ferredoxin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00465","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00465","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19549881","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1fiq

Chain	Residue	Details
A	GLN208
A	ARG351

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1fiq

Chain	Residue	Details
E	GLN208
E	ARG351

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1fiq

Chain	Residue	Details
B	GLU289

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1fiq

Chain	Residue	Details
F	GLU289

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