Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5ODI

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH

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	5
Details	binding site for residue ACT A 701

Chain	Residue
A	GLY367
A	VAL369
A	LYS377
A	LYS417
A	SER418

site_id	AC2
Number of Residues	33
Details	binding site for residue FAD A 702

Chain	Residue
A	VAL153
A	ALA154
A	VAL172
A	GLU173
A	LYS174
A	THR175
A	GLY180
A	ARG181
A	LEU185
A	THR188
A	PHE189
A	ALA327
A	ILE328
A	GLY329
A	TYR330
A	LEU353
A	TYR406
A	LYS409
A	SER500
A	GLY539
A	ALA540
A	LYS545
A	ASP546
A	ILE547
A	SER550
A	HOH803
A	HOH814
A	HOH820
G	LYS524
A	ILE149
A	GLY150
A	GLY151
A	GLY152

site_id	AC3
Number of Residues	8
Details	binding site for residue SF4 A 703

Chain	Residue
A	CYS386
A	ARG390
A	CYS399
A	SER400
A	CYS403
A	CYS404
A	ARG431
A	HOH831

site_id	AC4
Number of Residues	7
Details	binding site for residue SF4 A 704

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

site_id	AC5
Number of Residues	5
Details	binding site for residue SF4 A 705

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

site_id	AC6
Number of Residues	7
Details	binding site for residue SF4 A 706

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

site_id	AC7
Number of Residues	6
Details	binding site for residue SF4 A 707

Chain	Residue
A	CYS256
A	PRO257
A	CYS293
A	CYS296
A	GLY297
A	CYS299

site_id	AC8
Number of Residues	8
Details	binding site for residue SF4 A 708

Chain	Residue
A	CYS246
A	THR247
A	GLY248
A	CYS249
A	GLY250
A	CYS252
A	TYR286
A	CYS303

site_id	AC9
Number of Residues	5
Details	binding site for residue GOL A 709

Chain	Residue
A	VAL337
A	GLU340
A	LYS393
H	GLU168
I	GLU85

site_id	AD1
Number of Residues	8
Details	binding site for residue GOL A 710

Chain	Residue
A	TYR427
A	TYR441
A	PHE452
A	HOH842
A	HOH858
C	CYS34
C	TYR35
C	GLN36

site_id	AD2
Number of Residues	8
Details	binding site for residue 9S8 B 301

Chain	Residue
C	ALA127
B	GLY8
B	CYS9
B	CYS41
B	CYS42
B	CYS78
B	CYS81
B	PHE233

site_id	AD3
Number of Residues	8
Details	binding site for residue 9S8 B 302

Chain	Residue
B	HIS150
B	CYS153
B	HIS154
B	CYS193
B	CYS194
B	CYS231
B	CYS234
B	COM303

site_id	AD4
Number of Residues	10
Details	binding site for residue COM B 303

Chain	Residue
B	ALA44
B	PRO45
B	GLY46
B	GLY80
B	HIS154
B	GLY198
B	GLY199
B	PHE233
B	9S8302
B	HOH401

site_id	AD5
Number of Residues	8
Details	binding site for residue SF4 C 201

Chain	Residue
C	CYS34
C	TYR35
C	GLN36
C	CYS37
C	GLY38
C	CYS40
C	CYS87
C	VAL91

site_id	AD6
Number of Residues	9
Details	binding site for residue SF4 C 202

Chain	Residue
C	CYS44
C	PRO45
C	TYR52
C	THR54
C	CYS77
C	THR78
C	CYS80
C	TYR81
C	CYS83

site_id	AD7
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	AD8
Number of Residues	3
Details	binding site for residue ACT D 202

Chain	Residue
D	HIS104
D	GLU105
D	TRP106

site_id	AD9
Number of Residues	7
Details	binding site for residue TRS D 203

Chain	Residue
D	TRP4
D	GLY58
D	ASP60
D	PRO131
D	CYS132
D	LYS135
D	GLU136

site_id	AE1
Number of Residues	6
Details	binding site for residue SF4 E 301

Chain	Residue
E	CYS12
E	CYS15
E	CYS85
E	CYS149
E	HOH438
F	HIS163

site_id	AE2
Number of Residues	9
Details	binding site for residue SF4 E 302

Chain	Residue
E	LEU176
E	CYS224
E	PRO227
E	CYS228
E	CYS235
E	SER236
E	GLY237
E	CYS238
E	SER239

site_id	AE3
Number of Residues	6
Details	binding site for residue SF4 E 303

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

site_id	AE4
Number of Residues	11
Details	binding site for residue NFU F 501

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

site_id	AE5
Number of Residues	5
Details	binding site for residue FE F 502

Chain	Residue
F	GLU42
F	LEU395
F	HIS448
F	HOH605
F	HOH616

site_id	AE6
Number of Residues	5
Details	binding site for residue PE3 G 701

Chain	Residue
A	GLN144
A	MET165
A	PHE167
G	MET165
G	PHE167

site_id	AE7
Number of Residues	3
Details	binding site for residue ACT G 702

Chain	Residue
G	GLY141
G	THR143
G	ASN229

site_id	AE8
Number of Residues	31
Details	binding site for residue FAD G 703

Chain	Residue
G	GLY150
G	GLY151
G	GLY152
G	VAL153
G	ALA154
G	VAL172
G	GLU173
G	LYS174
G	THR175
G	GLY180
G	ARG181
G	LEU185
G	THR188
G	PHE189
G	ALA327
G	ILE328
G	GLY329
G	TYR330
G	GLU356
G	TYR406
G	LYS409
G	SER500
G	GLY539
G	ALA540
G	LYS545
G	ASP546
G	ILE547
G	PRO548
G	SER550
G	HOH823
G	HOH841

site_id	AE9
Number of Residues	7
Details	binding site for residue SF4 G 704

Chain	Residue
A	CYS197
G	CYS11
G	CYS13
G	TYR44
G	CYS46
G	CYS71
G	ARG100

site_id	AF1
Number of Residues	6
Details	binding site for residue SF4 G 705

Chain	Residue
G	CYS386
G	CYS399
G	SER400
G	CYS403
G	CYS404
G	HOH847

site_id	AF2
Number of Residues	6
Details	binding site for residue SF4 G 706

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

site_id	AF3
Number of Residues	6
Details	binding site for residue SF4 G 707

Chain	Residue
G	CYS256
G	PRO257
G	ALA273
G	CYS293
G	CYS296
G	CYS299

site_id	AF4
Number of Residues	11
Details	binding site for residue SF4 G 709

Chain	Residue
G	VAL579
G	CYS584
G	GLY585
G	GLY586
G	CYS587
G	GLY588
G	CYS590
G	ALA610
G	CYS627
G	SER629
G	LEU632

site_id	AF5
Number of Residues	7
Details	binding site for residue GOL G 710

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

site_id	AF6
Number of Residues	7
Details	binding site for residue 9S8 H 301

Chain	Residue
H	GLY8
H	CYS9
H	CYS41
H	CYS42
H	CYS78
H	CYS81
I	ALA127

site_id	AF7
Number of Residues	8
Details	binding site for residue 9S8 H 302

Chain	Residue
H	CYS153
H	HIS154
H	CYS193
H	CYS194
H	CYS231
H	PHE233
H	CYS234
H	COM303

site_id	AF8
Number of Residues	9
Details	binding site for residue COM H 303

Chain	Residue
H	ALA44
H	PRO45
H	GLY46
H	GLY80
H	HIS154
H	GLY198
H	GLY199
H	PHE233
H	9S8302

site_id	AF9
Number of Residues	2
Details	binding site for residue GOL H 304

Chain	Residue
H	ARG14
H	TYR15

site_id	AG1
Number of Residues	8
Details	binding site for residue SF4 I 201

Chain	Residue
I	CYS34
I	TYR35
I	GLN36
I	CYS37
I	GLY38
I	CYS40
I	CYS87
I	VAL91

site_id	AG2
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	THR79
I	CYS80
I	TYR81
I	CYS83

site_id	AG3
Number of Residues	7
Details	binding site for residue FES J 200

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

site_id	AG4
Number of Residues	6
Details	binding site for residue SF4 K 301

Chain	Residue
K	CYS12
K	GLY14
K	CYS15
K	CYS85
K	CYS149
L	HIS163

site_id	AG5
Number of Residues	8
Details	binding site for residue SF4 K 302

Chain	Residue
K	CYS224
K	PRO227
K	CYS228
K	CYS235
K	SER236
K	GLY237
K	CYS238
K	SER239

site_id	AG6
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	AG7
Number of Residues	2
Details	binding site for residue GOL K 304

Chain	Residue
K	ALA87
K	SER137

site_id	AG8
Number of Residues	11
Details	binding site for residue NFU L 501

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

site_id	AG9
Number of Residues	6
Details	binding site for residue FE L 502

Chain	Residue
L	GLU42
L	LYS273
L	LEU395
L	HIS448
L	HOH619
L	HOH623

site_id	AH1
Number of Residues	14
Details	binding site for Di-peptide SF4 G 708 and CYS G 617

Chain	Residue
G	ILE576
G	CYS594
G	ALA598
G	PRO599
G	VAL612
G	ILE613
G	SER614
G	ALA615
G	LEU616
G	LYS618
G	GLY619
G	CYS620
G	GLY621
G	CYS623

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. CtGCGqCSeVCP

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

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)