Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3HYW

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone

Replaces: 3H28

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0019646	biological_process	aerobic electron transport chain
A	0042802	molecular_function	identical protein binding
A	0048038	molecular_function	quinone binding
A	0070224	molecular_function	sulfide:quinone oxidoreductase activity
B	0000166	molecular_function	nucleotide binding
B	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0019646	biological_process	aerobic electron transport chain
B	0042802	molecular_function	identical protein binding
B	0048038	molecular_function	quinone binding
B	0070224	molecular_function	sulfide:quinone oxidoreductase activity
C	0000166	molecular_function	nucleotide binding
C	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0019646	biological_process	aerobic electron transport chain
C	0042802	molecular_function	identical protein binding
C	0048038	molecular_function	quinone binding
C	0070224	molecular_function	sulfide:quinone oxidoreductase activity
D	0000166	molecular_function	nucleotide binding
D	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
D	0016020	cellular_component	membrane
D	0016491	molecular_function	oxidoreductase activity
D	0019646	biological_process	aerobic electron transport chain
D	0042802	molecular_function	identical protein binding
D	0048038	molecular_function	quinone binding
D	0070224	molecular_function	sulfide:quinone oxidoreductase activity
E	0000166	molecular_function	nucleotide binding
E	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
E	0016020	cellular_component	membrane
E	0016491	molecular_function	oxidoreductase activity
E	0019646	biological_process	aerobic electron transport chain
E	0042802	molecular_function	identical protein binding
E	0048038	molecular_function	quinone binding
E	0070224	molecular_function	sulfide:quinone oxidoreductase activity
F	0000166	molecular_function	nucleotide binding
F	0003955	molecular_function	NAD(P)H dehydrogenase (quinone) activity
F	0016020	cellular_component	membrane
F	0016491	molecular_function	oxidoreductase activity
F	0019646	biological_process	aerobic electron transport chain
F	0042802	molecular_function	identical protein binding
F	0048038	molecular_function	quinone binding
F	0070224	molecular_function	sulfide:quinone oxidoreductase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	40
Details	BINDING SITE FOR RESIDUE FAD A 441

Chain	Residue
A	ILE8
A	THR42
A	PRO43
A	LYS77
A	ALA78
A	ALA104
A	THR105
A	GLY106
A	ILE123
A	CYS124
A	PRO159
A	GLY9
A	GLY293
A	VAL294
A	LYS312
A	THR313
A	GLY314
A	ILE317
A	LYS382
A	SO4433
A	HOH437
A	HOH439
A	GLY10
A	HOH453
A	HOH458
A	DCQ500
A	HOH513
A	HOH515
A	H2S700
A	PS9800
A	HOH1162
A	HOH1247
A	HOH1509
A	GLY11
A	HOH1512
A	VAL12
A	GLY13
A	SER34
A	ASP35
A	ARG36

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DCQ A 500

Chain	Residue
A	GLY314
A	MET315
A	GLU318
A	ILE346
A	PHE381
A	PHE385
A	PHE402
A	GLU403
A	FAD441
A	LMT600
A	HOH1162
A	HOH1514
B	DCQ500

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT A 600

Chain	Residue
A	LYS373
A	TRP377
A	PHE381
A	PHE410
A	SO4434
A	DCQ500
B	LMT600

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE H2S A 700

Chain	Residue
A	CYS124
A	MET251
A	FAD441

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PS9 A 800

Chain	Residue
A	CSS156
A	PHE157
A	GLY158
A	PRO159
A	CSS347
A	FAD441

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 431

Chain	Residue
A	ARG369
A	LYS412
E	LYS172
E	HOH589

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 432

Chain	Residue
A	TRP391
A	ARG394
A	ASN395
A	HOH436
A	HOH1182
A	HOH1434
B	SER401

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 433

Chain	Residue
A	LYS77
A	LYS108
A	PRO257
A	GLU258
A	VAL259
A	FAD441
A	HOH515
A	HOH616
A	HOH1359

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 434

Chain	Residue
A	GLY375
A	LYS376
A	TRP377
A	LMT600

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 435

Chain	Residue
A	LYS172
A	HOH1315
C	ARG369

site_id	BC2
Number of Residues	41
Details	BINDING SITE FOR RESIDUE FAD B 441

Chain	Residue
B	GLY11
B	VAL12
B	GLY13
B	SER34
B	ASP35
B	ARG36
B	THR42
B	PRO43
B	LYS77
B	ALA78
B	ALA104
B	THR105
B	GLY106
B	ILE123
B	CYS124
B	PRO159
B	GLY293
B	VAL294
B	LYS312
B	THR313
B	GLY314
B	ILE317
B	CSS347
B	LYS382
B	HOH435
B	HOH442
B	HOH443
B	HOH446
B	HOH449
B	HOH461
B	HOH489
B	DCQ500
B	H2S700
B	HOH740
B	PS9802
B	HOH984
B	HOH1515
B	HOH1518
B	ILE8
B	GLY9
B	GLY10

site_id	BC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE DCQ B 500

Chain	Residue
A	DCQ500
B	MET315
B	GLU318
B	ILE346
B	ILE348
B	PHE381
B	PHE385
B	TYR388
B	PHE402
B	GLU403
B	LEU407
B	FAD441
B	HOH446
B	LMT600
B	HOH1518
B	HOH1519

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE LMT B 600

Chain	Residue
A	PHE381
A	LMT600
B	LYS373
B	TRP377
B	PHE381
B	PHE410
B	SO4434
B	DCQ500
B	HOH605

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE H2S B 700

Chain	Residue
B	CYS124
B	FAD441

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PS9 B 800

Chain	Residue
B	CSS156
B	PHE157
B	GLY158

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PS9 B 802

Chain	Residue
B	GLY158
B	PRO159
B	GLU162
B	CSS347
B	ILE348
B	FAD441

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 431

Chain	Residue
B	ARG369
B	LYS412
D	LYS172

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 432

Chain	Residue
A	SER401
B	TRP391
B	ARG394
B	ASN395
B	HOH447
B	HOH1457
B	HOH1480

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 433

Chain	Residue
B	LYS77
B	LYS108
B	PRO257
B	GLU258

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 434

Chain	Residue
B	GLY375
B	LYS376
B	TRP377
B	LMT600
B	HOH1329

site_id	CC3
Number of Residues	39
Details	BINDING SITE FOR RESIDUE FAD C 441

Chain	Residue
C	GLY9
C	GLY10
C	GLY11
C	VAL12
C	GLY13
C	SER34
C	ASP35
C	ARG36
C	THR42
C	PRO43
C	LYS77
C	ALA78
C	ALA104
C	THR105
C	GLY106
C	ILE123
C	CYS124
C	PRO159
C	GLY293
C	VAL294
C	LYS312
C	THR313
C	GLY314
C	ILE317
C	LYS382
C	SO4433
C	HOH435
C	HOH439
C	HOH442
C	HOH457
C	HOH459
C	HOH466
C	HOH487
C	DCQ500
C	HOH641
C	H2S700
C	HOH770
C	PS9800
C	HOH1027

site_id	CC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DCQ C 500

Chain	Residue
C	GLY314
C	MET315
C	GLU318
C	ILE346
C	PHE381
C	PHE385
C	TYR388
C	GLU403
C	FAD441
C	HOH459
C	HOH502
D	TYR388
D	DCQ500

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT C 600

Chain	Residue
C	LYS373
C	TRP377
C	PHE381
C	SO4434
D	LMT600

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE H2S C 700

Chain	Residue
C	CYS124
C	FAD441

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PS9 C 800

Chain	Residue
C	CSS156
C	GLY158
C	PRO159
C	CSS347
C	ILE348
C	ALA349
C	FAD441

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 432

Chain	Residue
C	TRP391
C	ARG394
C	ASN395
C	HOH1155
D	SER401

site_id	CC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 433

Chain	Residue
C	LYS77
C	LYS108
C	PRO257
C	GLU258
C	VAL259
C	FAD441
C	HOH641
C	HOH665

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 434

Chain	Residue
C	GLY375
C	LYS376
C	TRP377
C	LMT600

site_id	DC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 C 431

Chain	Residue
C	LYS172
E	ARG369

site_id	DC3
Number of Residues	38
Details	BINDING SITE FOR RESIDUE FAD D 441

Chain	Residue
D	ILE8
D	GLY9
D	GLY10
D	GLY11
D	VAL12
D	GLY13
D	SER34
D	ASP35
D	ARG36
D	THR42
D	PRO43
D	LYS77
D	ALA78
D	ALA104
D	THR105
D	GLY106
D	ILE123
D	CYS124
D	PRO159
D	VAL259
D	GLY293
D	VAL294
D	LYS312
D	THR313
D	GLY314
D	ILE317
D	LYS382
D	HOH437
D	HOH443
D	HOH445
D	HOH466
D	DCQ500
D	HOH513
D	H2S700
D	HOH900
D	HOH1171
D	HOH1326
D	HOH1347

site_id	DC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DCQ D 500

Chain	Residue
C	DCQ500
D	GLY314
D	MET315
D	GLU318
D	ILE346
D	PHE381
D	PHE385
D	PHE402
D	GLU403
D	FAD441
D	HOH443
D	LMT600

site_id	DC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT D 600

Chain	Residue
C	PHE381
C	LMT600
D	LYS373
D	TRP377
D	PHE381
D	SO4434
D	DCQ500

site_id	DC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE H2S D 700

Chain	Residue
D	CYS124
D	CSS156
D	FAD441

site_id	DC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PS9 D 800

Chain	Residue
D	CSS156
D	GLY158
D	PS9802

site_id	DC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PS9 D 802

Chain	Residue
D	CSS347
D	PS9800

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 431

Chain	Residue
D	ARG369
D	LYS412
F	LYS172

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 432

Chain	Residue
C	SER401
D	TRP391
D	ARG394
D	ASN395
D	HOH478

site_id	EC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 433

Chain	Residue
D	LYS77
D	LYS108
D	PRO257
D	GLU258

site_id	EC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 434

Chain	Residue
D	MET374
D	GLY375
D	LYS376
D	LMT600

site_id	EC4
Number of Residues	37
Details	BINDING SITE FOR RESIDUE FAD E 441

Chain	Residue
E	ILE8
E	GLY9
E	GLY10
E	GLY11
E	VAL12
E	GLY13
E	SER34
E	ASP35
E	ARG36
E	THR42
E	PRO43
E	LYS77
E	ALA78
E	ALA104
E	THR105
E	GLY106
E	ILE123
E	CYS124
E	GLY293
E	VAL294
E	LYS312
E	THR313
E	GLY314
E	LYS382
E	SO4433
E	HOH436
E	HOH444
E	HOH446
E	HOH459
E	HOH461
E	HOH474
E	DCQ500
E	H2S700
E	PS9800
E	HOH1328
E	HOH1365
E	HOH1526

site_id	EC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DCQ E 500

Chain	Residue
E	GLY314
E	MET315
E	GLU318
E	ILE346
E	PHE381
E	PHE385
E	PHE402
E	FAD441
E	HOH1528
F	DCQ500

site_id	EC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT E 600

Chain	Residue
E	LYS373
E	TRP377
E	PHE381
E	LEU411
E	SO4434
E	HOH435
F	LMT600

site_id	EC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE H2S E 700

Chain	Residue
E	CYS124
E	FAD441

site_id	EC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PS9 E 800

Chain	Residue
E	CSS156
E	GLY158
E	PRO159
E	CSS347
E	FAD441

site_id	EC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 E 432

Chain	Residue
E	TRP391
E	ARG394
E	ASN395
E	HOH488
E	HOH720
E	HOH1363
E	HOH1387
F	SER401

site_id	FC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 433

Chain	Residue
E	LYS77
E	LYS108
E	PRO257
E	GLU258
E	VAL259
E	FAD441
E	HOH1354

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 434

Chain	Residue
E	GLY375
E	LYS376
E	TRP377
E	LMT600

site_id	FC3
Number of Residues	41
Details	BINDING SITE FOR RESIDUE FAD F 441

Chain	Residue
F	ILE8
F	GLY9
F	GLY10
F	GLY11
F	VAL12
F	GLY13
F	SER34
F	ASP35
F	ARG36
F	THR42
F	PRO43
F	LYS77
F	ALA78
F	ALA104
F	THR105
F	GLY106
F	ILE123
F	CYS124
F	PRO159
F	GLY293
F	VAL294
F	LYS312
F	THR313
F	GLY314
F	ILE317
F	LYS382
F	SO4433
F	HOH435
F	HOH436
F	HOH438
F	HOH462
F	HOH498
F	DCQ500
F	HOH506
F	HOH658
F	H2S700
F	PS9800
F	HOH1377
F	HOH1448
F	HOH1529
F	HOH1532

site_id	FC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DCQ F 500

Chain	Residue
E	DCQ500
F	GLY314
F	MET315
F	GLU318
F	ILE346
F	ILE348
F	PHE381
F	PHE385
F	GLU403
F	FAD441
F	LMT600
F	HOH1531
F	HOH1532

site_id	FC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE LMT F 600

Chain	Residue
E	PHE381
E	LMT600
F	LYS373
F	PHE381
F	SO4434
F	DCQ500

site_id	FC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE H2S F 700

Chain	Residue
F	CYS124
F	FAD441

site_id	FC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PS9 F 800

Chain	Residue
F	CSS156
F	GLY158
F	PRO159
F	CSS347
F	ILE348
F	FAD441

site_id	FC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 F 431

Chain	Residue
B	LYS172
F	ARG369

site_id	FC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 F 432

Chain	Residue
E	SER401
F	TRP391
F	ARG394
F	ASN395
F	HOH446
F	HOH714

site_id	GC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 F 433

Chain	Residue
F	LYS77
F	LYS108
F	PRO257
F	GLU258
F	VAL259
F	FAD441

site_id	GC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 F 434

Chain	Residue
F	GLY375
F	LYS376
F	TRP377
F	LMT600

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	ACT_SITE: Cysteine persulfide intermediate => ECO:0000250\|UniProtKB:Q7ZAG8, ECO:0000303\|PubMed:19487671

Chain	Residue	Details
A	CSS156
E	CSS347
F	CSS156
F	CSS347
A	CSS347
B	CSS156
B	CSS347
C	CSS156
C	CSS347
D	CSS156
D	CSS347
E	CSS156

site_id	SWS_FT_FI2
Number of Residues	48
Details	BINDING: BINDING => ECO:0000269\|PubMed:19487671

Chain	Residue	Details
A	GLY9
B	SER34
B	THR42
B	THR105
B	VAL294
B	GLY314
B	ILE346
B	LYS382
C	GLY9
C	SER34
C	THR42
A	SER34
C	THR105
C	VAL294
C	GLY314
C	ILE346
C	LYS382
D	GLY9
D	SER34
D	THR42
D	THR105
D	VAL294
A	THR42
D	GLY314
D	ILE346
D	LYS382
E	GLY9
E	SER34
E	THR42
E	THR105
E	VAL294
E	GLY314
E	ILE346
A	THR105
E	LYS382
F	GLY9
F	SER34
F	THR42
F	THR105
F	VAL294
F	GLY314
F	ILE346
F	LYS382
A	VAL294
A	GLY314
A	ILE346
A	LYS382
B	GLY9

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