Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5ODC

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus at 2.3 A resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0016491	molecular_function	oxidoreductase activity
A	0046872	molecular_function	metal ion binding
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0015948	biological_process	methanogenesis
B	0016491	molecular_function	oxidoreductase activity
B	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
C	0005886	cellular_component	plasma membrane
C	0015948	biological_process	methanogenesis
C	0016491	molecular_function	oxidoreductase activity
C	0046872	molecular_function	metal ion binding
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
D	0016491	molecular_function	oxidoreductase activity
D	0046872	molecular_function	metal ion binding
D	0051536	molecular_function	iron-sulfur cluster binding
D	0051537	molecular_function	2 iron, 2 sulfur cluster binding
D	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
E	0016491	molecular_function	oxidoreductase activity
E	0033748	molecular_function	hydrogenase (acceptor) activity
E	0046872	molecular_function	metal ion binding
E	0047985	molecular_function	hydrogen dehydrogenase activity
E	0051536	molecular_function	iron-sulfur cluster binding
E	0051539	molecular_function	4 iron, 4 sulfur cluster binding
F	0008901	molecular_function	ferredoxin hydrogenase activity
F	0016151	molecular_function	nickel cation binding
F	0016491	molecular_function	oxidoreductase activity
F	0033748	molecular_function	hydrogenase (acceptor) activity
F	0046872	molecular_function	metal ion binding
F	0047985	molecular_function	hydrogen dehydrogenase activity
G	0000166	molecular_function	nucleotide binding
G	0016491	molecular_function	oxidoreductase activity
G	0046872	molecular_function	metal ion binding
G	0051536	molecular_function	iron-sulfur cluster binding
G	0051539	molecular_function	4 iron, 4 sulfur cluster binding
H	0015948	biological_process	methanogenesis
H	0016491	molecular_function	oxidoreductase activity
H	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
I	0005886	cellular_component	plasma membrane
I	0015948	biological_process	methanogenesis
I	0016491	molecular_function	oxidoreductase activity
I	0046872	molecular_function	metal ion binding
I	0051536	molecular_function	iron-sulfur cluster binding
I	0051539	molecular_function	4 iron, 4 sulfur cluster binding
I	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
J	0016491	molecular_function	oxidoreductase activity
J	0046872	molecular_function	metal ion binding
J	0051536	molecular_function	iron-sulfur cluster binding
J	0051537	molecular_function	2 iron, 2 sulfur cluster binding
J	0051912	molecular_function	CoB--CoM heterodisulfide reductase activity
K	0016491	molecular_function	oxidoreductase activity
K	0033748	molecular_function	hydrogenase (acceptor) activity
K	0046872	molecular_function	metal ion binding
K	0047985	molecular_function	hydrogen dehydrogenase activity
K	0051536	molecular_function	iron-sulfur cluster binding
K	0051539	molecular_function	4 iron, 4 sulfur cluster binding
L	0008901	molecular_function	ferredoxin hydrogenase activity
L	0016151	molecular_function	nickel cation binding
L	0016491	molecular_function	oxidoreductase activity
L	0033748	molecular_function	hydrogenase (acceptor) activity
L	0046872	molecular_function	metal ion binding
L	0047985	molecular_function	hydrogen dehydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	40
Details	binding site for residue FAD A 701

Chain	Residue
A	ILE149
A	GLY180
A	ARG181
A	LEU185
A	LYS187
A	THR188
A	PHE189
A	ALA327
A	ILE328
A	GLY329
A	TYR330
A	GLY150
A	ALA352
A	LEU353
A	GLU356
A	TYR406
A	LYS409
A	MET495
A	SER500
A	VAL504
A	GLY539
A	ALA540
A	GLY151
A	LYS545
A	ASP546
A	ILE547
A	PRO548
A	SER550
A	HOH806
A	HOH821
A	HOH824
A	HOH851
A	HOH853
A	GLY152
A	HOH860
A	VAL153
A	ALA154
A	GLU173
A	LYS174
A	THR175

site_id	AC2
Number of Residues	1
Details	binding site for residue NA A 702

Chain	Residue
A	ASP164

site_id	AC3
Number of Residues	3
Details	binding site for residue ACT A 703

Chain	Residue
A	GLN553
G	PRO548
G	ALA549

site_id	AC4
Number of Residues	5
Details	binding site for residue PE3 A 704

Chain	Residue
A	MET165
A	PHE167
G	MET165
G	PHE167
G	ALA566

site_id	AC5
Number of Residues	7
Details	binding site for residue SF4 A 705

Chain	Residue
A	CYS11
A	CYS13
A	CYS46
A	CYS71
A	HIS76
A	ARG100
G	CYS197

site_id	AC6
Number of Residues	6
Details	binding site for residue SF4 A 706

Chain	Residue
A	CYS246
A	THR247
A	CYS249
A	GLY250
A	CYS252
A	CYS303

site_id	AC7
Number of Residues	4
Details	binding site for residue SF4 A 707

Chain	Residue
A	CYS256
A	CYS293
A	CYS296
A	CYS299

site_id	AC8
Number of Residues	7
Details	binding site for residue SF4 A 708

Chain	Residue
A	GLN385
A	CYS386
A	SER389
A	CYS399
A	SER400
A	CYS403
A	CYS404

site_id	AC9
Number of Residues	8
Details	binding site for residue SF4 A 709

Chain	Residue
A	CYS584
A	CYS587
A	GLY588
A	CYS590
A	ALA610
A	CYS627
A	SER629
A	LEU632

site_id	AD1
Number of Residues	6
Details	binding site for residue SF4 A 710

Chain	Residue
A	CYS594
A	CYS617
A	LYS618
A	CYS620
A	GLY621
A	CYS623

site_id	AD2
Number of Residues	8
Details	binding site for residue GOL A 711

Chain	Residue
A	TYR427
A	TYR441
A	PHE452
A	LEU477
A	HOH801
C	CYS34
C	TYR35
C	GLN36

site_id	AD3
Number of Residues	7
Details	binding site for residue GOL A 712

Chain	Residue
A	HIS636
A	PHE637
D	ARG39
A	GLU77
A	ARG81
A	GLU573
A	ILE575

site_id	AD4
Number of Residues	4
Details	binding site for residue GOL A 713

Chain	Residue
A	ASP25
A	PHE29
A	THR32
A	LYS119

site_id	AD5
Number of Residues	6
Details	binding site for residue GOL A 714

Chain	Residue
A	LYS236
A	LYS237
A	ARG239
A	GLN312
A	GLU313
A	GLU315

site_id	AD6
Number of Residues	6
Details	binding site for residue 9S8 B 301

Chain	Residue
B	HIS150
B	CYS153
B	CYS193
B	CYS194
B	CYS231
B	CYS234

site_id	AD7
Number of Residues	7
Details	binding site for residue 9S8 B 302

Chain	Residue
B	GLY8
B	CYS9
B	CYS41
B	CYS42
B	CYS78
B	CYS81
C	ALA127

site_id	AD8
Number of Residues	2
Details	binding site for residue ACT B 303

Chain	Residue
B	LYS2
B	GLY71

site_id	AD9
Number of Residues	3
Details	binding site for residue GOL B 304

Chain	Residue
B	GLY46
B	GLY198
B	PHE233

site_id	AE1
Number of Residues	6
Details	binding site for residue SF4 C 201

Chain	Residue
C	CYS34
C	TYR35
C	CYS37
C	GLY38
C	CYS40
C	CYS87

site_id	AE2
Number of Residues	9
Details	binding site for residue SF4 C 202

Chain	Residue
C	CYS44
C	TYR52
C	THR54
C	CYS77
C	THR78
C	CYS80
C	TYR81
C	CYS83
C	THR94

site_id	AE3
Number of Residues	6
Details	binding site for residue GOL C 203

Chain	Residue
C	ARG53
C	LYS56
C	VAL57
C	LYS60
C	SER71
C	ASP73

site_id	AE4
Number of Residues	7
Details	binding site for residue FES D 201

Chain	Residue
D	CYS13
D	MET41
D	CYS42
D	SER43
D	CYS67
D	CYS72
D	HIS73

site_id	AE5
Number of Residues	7
Details	binding site for residue TRS D 202

Chain	Residue
D	TRP4
D	LYS7
D	GLY58
D	ASP60
D	CYS132
D	LYS133
D	GLU136

site_id	AE6
Number of Residues	5
Details	binding site for residue GOL D 203

Chain	Residue
D	HIS104
D	GLU105
D	TRP106
D	HOH301
D	HOH329

site_id	AE7
Number of Residues	7
Details	binding site for residue SF4 E 301

Chain	Residue
E	CYS12
E	GLY14
E	CYS15
E	THR84
E	CYS85
E	CYS149
F	HIS163

site_id	AE8
Number of Residues	6
Details	binding site for residue SF4 E 302

Chain	Residue
E	CYS177
E	CYS180
E	LYS184
E	CYS207
E	LEU208
E	CYS215

site_id	AE9
Number of Residues	8
Details	binding site for residue SF4 E 303

Chain	Residue
E	LEU176
E	CYS224
E	CYS228
E	CYS235
E	SER236
E	CYS238
E	SER239
F	ARG160

site_id	AF1
Number of Residues	3
Details	binding site for residue GOL E 304

Chain	Residue
E	ALA87
E	SER137
E	PHE145

site_id	AF2
Number of Residues	6
Details	binding site for residue CA F 501

Chain	Residue
F	GLU42
F	LEU395
F	HIS448
F	HOH611
F	HOH612
F	HOH634

site_id	AF3
Number of Residues	5
Details	binding site for residue MG F 502

Chain	Residue
E	ASP279
F	ARG48
F	TYR49
F	ASP52
F	TYR56

site_id	AF4
Number of Residues	3
Details	binding site for residue ACT F 503

Chain	Residue
F	GLY247
F	ASP299
F	LYS319

site_id	AF5
Number of Residues	12
Details	binding site for residue NFU F 504

Chain	Residue
F	CYS61
F	CYS64
F	HIS68
F	ALA373
F	PRO374
F	ARG375
F	LEU378
F	VAL397
F	ALA398
F	THR399
F	CYS442
F	CYS445

site_id	AF6
Number of Residues	39
Details	binding site for residue FAD G 701

Chain	Residue
G	GLY150
G	GLY152
G	VAL153
G	ALA154
G	VAL172
G	GLU173
G	LYS174
G	THR175
G	GLY180
G	ARG181
G	MET182
G	LEU185
G	THR188
G	PHE189
G	ALA327
G	ILE328
G	GLY329
G	TYR330
G	LEU353
G	GLU356
G	TYR406
G	LYS409
G	MET495
G	SER500
G	VAL504
G	GLY539
G	ALA540
G	LYS545
G	ASP546
G	ILE547
G	PRO548
G	SER550
G	HOH803
G	HOH808
G	HOH811
G	HOH858
G	HOH864
G	HOH885
G	HOH931

site_id	AF7
Number of Residues	6
Details	binding site for residue NA G 702

Chain	Residue
G	VAL206
G	ALA207
G	LYS208
G	HIS209
G	VAL212
G	HOH876

site_id	AF8
Number of Residues	4
Details	binding site for residue ACT G 703

Chain	Residue
B	GLU168
G	VAL337
G	GLU339
G	GLU340

site_id	AF9
Number of Residues	6
Details	binding site for residue ACT G 704

Chain	Residue
A	PRO548
A	ALA549
A	ALA552
A	HOH886
G	GLN542
G	GLN553

site_id	AG1
Number of Residues	7
Details	binding site for residue SF4 G 705

Chain	Residue
G	CYS584
G	CYS587
G	GLY588
G	CYS590
G	CYS627
G	SER629
K	ASN175

site_id	AG2
Number of Residues	7
Details	binding site for residue SF4 G 706

Chain	Residue
A	CYS197
G	CYS11
G	CYS13
G	CYS46
G	CYS71
G	HIS76
G	ARG100

site_id	AG3
Number of Residues	6
Details	binding site for residue SF4 G 707

Chain	Residue
G	CYS256
G	CYS293
G	ILE294
G	GLU295
G	CYS296
G	CYS299

site_id	AG4
Number of Residues	8
Details	binding site for residue SF4 G 708

Chain	Residue
G	CYS386
G	SER389
G	ARG390
G	CYS399
G	SER400
G	ASN401
G	CYS403
G	CYS404

site_id	AG5
Number of Residues	6
Details	binding site for residue SF4 G 709

Chain	Residue
G	CYS246
G	THR247
G	CYS249
G	GLY250
G	CYS252
G	CYS303

site_id	AG6
Number of Residues	6
Details	binding site for residue SF4 G 710

Chain	Residue
G	CYS594
G	CYS617
G	LYS618
G	CYS620
G	GLY621
G	CYS623

site_id	AG7
Number of Residues	7
Details	binding site for residue GOL G 711

Chain	Residue
G	TYR427
G	TYR441
G	PHE452
G	LEU477
I	CYS34
I	TYR35
I	GLN36

site_id	AG8
Number of Residues	5
Details	binding site for residue GOL G 712

Chain	Residue
G	GLU77
G	ARG81
G	GLU573
G	HIS636
J	ARG39

site_id	AG9
Number of Residues	4
Details	binding site for residue GOL G 713

Chain	Residue
G	THR175
G	ARG181
G	PHE264
G	HOH887

site_id	AH1
Number of Residues	7
Details	binding site for residue GOL G 714

Chain	Residue
G	LYS236
G	LYS237
G	ILE241
G	GLU243
G	GLN312
G	GLU313
G	GLU315

site_id	AH2
Number of Residues	6
Details	binding site for residue 9S8 H 301

Chain	Residue
H	GLY8
H	CYS9
H	CYS41
H	CYS42
H	CYS78
H	CYS81

site_id	AH3
Number of Residues	6
Details	binding site for residue 9S8 H 302

Chain	Residue
H	HIS150
H	CYS153
H	CYS193
H	CYS194
H	CYS231
H	CYS234

site_id	AH4
Number of Residues	3
Details	binding site for residue MG I 201

Chain	Residue
I	ARG53
I	ASP73
I	HOH321

site_id	AH5
Number of Residues	9
Details	binding site for residue SF4 I 202

Chain	Residue
I	CYS44
I	TYR52
I	THR54
I	CYS77
I	THR78
I	CYS80
I	TYR81
I	CYS83
I	THR94

site_id	AH6
Number of Residues	6
Details	binding site for residue SF4 I 203

Chain	Residue
I	CYS34
I	TYR35
I	CYS37
I	GLY38
I	CYS40
I	CYS87

site_id	AH7
Number of Residues	8
Details	binding site for residue FES J 201

Chain	Residue
J	CYS13
J	MET41
J	CYS42
J	SER43
J	CYS67
J	CYS72
J	HIS73
J	TYR74

site_id	AH8
Number of Residues	8
Details	binding site for residue SF4 K 301

Chain	Residue
K	CYS12
K	CYS15
K	THR84
K	CYS85
K	GLY148
K	CYS149
L	ARG59
L	HIS163

site_id	AH9
Number of Residues	7
Details	binding site for residue SF4 K 302

Chain	Residue
K	LEU176
K	CYS224
K	CYS228
K	CYS235
K	SER236
K	CYS238
L	ARG160

site_id	AI1
Number of Residues	6
Details	binding site for residue SF4 K 303

Chain	Residue
K	CYS177
K	CYS180
K	LYS184
K	CYS207
K	LEU208
K	CYS215

site_id	AI2
Number of Residues	7
Details	binding site for residue GOL K 304

Chain	Residue
K	PHE88
K	ARG221
K	PRO241
K	THR242
K	VAL245
K	VAL246
K	GOL305

site_id	AI3
Number of Residues	4
Details	binding site for residue GOL K 305

Chain	Residue
K	ALA87
K	SER137
K	PHE145
K	GOL304

site_id	AI4
Number of Residues	5
Details	binding site for residue GOL K 306

Chain	Residue
K	THR7
K	HIS37
K	LYS45
K	ILE68
L	PRO8

site_id	AI5
Number of Residues	6
Details	binding site for residue CA L 501

Chain	Residue
L	GLU42
L	LEU395
L	HIS448
L	HOH606
L	HOH613
L	HOH623

site_id	AI6
Number of Residues	12
Details	binding site for residue NFU L 502

Chain	Residue
L	CYS61
L	CYS64
L	HIS68
L	ALA373
L	PRO374
L	ARG375
L	LEU378
L	VAL397
L	ALA398
L	THR399
L	CYS442
L	CYS445

Functional Information from PROSITE/UniProt

site_id	PS00198
Number of Residues	12
Details	4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CyQCGtCTgSCP

Chain	Residue	Details
C	CYS34-PRO45
C	CYS77-PRO88
A	CYS246-PRO257
A	CYS293-GLY304
A	CYS584-PRO595

site_id	PS00507
Number of Residues	26
Details	NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGFEkflegryvedapiytPRiCGIC

Chain	Residue	Details
F	ARG39-CYS64

site_id	PS00508
Number of Residues	10
Details	NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. YDPCLSCat.H

Chain	Residue	Details
F	TYR439-HIS448

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