Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4UD6

Structure of methylviologen-treated anaerobically purified D. fructosovorans NiFe-hydrogenase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0051536	molecular_function	iron-sulfur cluster binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0009375	cellular_component	ferredoxin hydrogenase complex
B	0051536	molecular_function	iron-sulfur cluster binding
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0051536	molecular_function	iron-sulfur cluster binding
Q	0008901	molecular_function	ferredoxin hydrogenase activity
Q	0016151	molecular_function	nickel cation binding
Q	0016491	molecular_function	oxidoreductase activity
Q	0046872	molecular_function	metal ion binding
R	0008901	molecular_function	ferredoxin hydrogenase activity
R	0016151	molecular_function	nickel cation binding
R	0016491	molecular_function	oxidoreductase activity
R	0046872	molecular_function	metal ion binding
S	0008901	molecular_function	ferredoxin hydrogenase activity
S	0016151	molecular_function	nickel cation binding
S	0016491	molecular_function	oxidoreductase activity
S	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 A 1265

Chain	Residue
A	HIS184
A	CYS187
A	ARG189
A	LEU190
A	CYS212
A	LEU213
A	CYS218
A	PRO221

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S A 1266

Chain	Residue
A	CYS227
A	PHE232
A	TRP237
A	CYS245
A	LEU246
A	CYS248
Q	LYS225
Q	GLN230
A	ASN225

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 A 1267

Chain	Residue
A	GLU16
A	CYS17
A	CYS20
A	GLY112
A	THR113
A	CYS114
A	GLY146
A	CYS147
Q	ARG70
Q	HIS228

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 1271

Chain	Residue
A	ASP168
A	LEU169
A	LYS176
A	GOL1272
A	HOH2213
A	HOH2323

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 1272

Chain	Residue
A	LYS140
A	LEU169
A	ASP170
A	GOL1271
A	HOH2324

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 1273

Chain	Residue
A	ARG6
A	LEU37
A	ASP38
A	HOH2325
Q	ALA169
Q	PHE170

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 B 1265

Chain	Residue
B	HIS184
B	CYS187
B	ARG189
B	LEU190
B	PHE193
B	CYS212
B	LEU213
B	CYS218

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S B 1266

Chain	Residue
B	ASN225
B	CYS227
B	PHE232
B	CYS245
B	LEU246
B	CYS248
R	LYS225
R	GLN230

site_id	AC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SF4 B 1267

Chain	Residue
B	GLU16
B	CYS17
B	CYS20
B	GLY112
B	THR113
B	CYS114
B	GLY146
B	CYS147
B	PRO148
R	ARG70
R	HIS228

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 C 1265

Chain	Residue
C	HIS184
C	CYS187
C	ARG189
C	LEU190
C	CYS212
C	LEU213
C	CYS218
C	PRO221

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S C 1266

Chain	Residue
C	ASN225
C	CYS227
C	PHE232
C	TRP237
C	CYS245
C	LEU246
C	CYS248
S	LYS225
S	GLN230

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 C 1267

Chain	Residue
C	CYS17
C	CYS20
C	THR113
C	CYS114
C	GLY146
C	CYS147
C	PRO148
S	ARG70
S	HIS228

site_id	BC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO Q 1550

Chain	Residue
Q	HIS79
Q	ALA474
Q	PRO475
Q	ARG476
Q	LEU479
Q	VAL497
Q	PRO498
Q	SER499
Q	CSO543
Q	CYS546
Q	NI1551
Q	CYS75
Q	VAL78

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI Q 1551

Chain	Residue
Q	CYS72
Q	CYS75
Q	CSO543
Q	CYS546
Q	FCO1550

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG Q 1553

Chain	Residue
Q	GLU53
Q	LEU495
Q	HIS549
Q	HOH2051
Q	HOH2052
Q	HOH2312

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL Q 1561

Chain	Residue
Q	ARG100
Q	ASN104
Q	PHE295
Q	ALA296
Q	THR297
Q	GLU445
Q	HOH2112
Q	HOH2442

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL Q 1562

Chain	Residue
A	ALA55
C	PHE198
C	HOH2176
C	HOH2200
Q	ASN181
Q	ALA182
Q	LEU185
Q	ARG529

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL Q 1563

Chain	Residue
Q	GLY281
Q	GLY282
Q	ILE283
Q	GLY284
Q	GLY285
Q	ARG319
Q	HIS419
Q	HOH2370
Q	HOH2443

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL Q 1564

Chain	Residue
Q	LYS245
Q	LYS337
Q	TYR338
Q	ASP366
Q	HOH2444

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL R 1001

Chain	Residue
R	GLY281
R	GLY282
R	ILE283
R	GLY284
R	GLY285
R	ARG319
R	HIS419
R	HOH2259

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL R 1002

Chain	Residue
R	THR286
R	SER287
R	ASN288
R	ALA380
R	PRO514
R	GLU517
R	HOH2225
R	HOH2380

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL R 1003

Chain	Residue
R	ARG152
R	PRO153
R	SER156
R	HOH2130
R	HOH2137
S	ALA451

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL R 1004

Chain	Residue
C	ALA103
R	GLU465
R	SER466
R	LYS467
R	ARG484
R	HOH2366
R	HOH2367

site_id	CC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO R 1550

Chain	Residue
R	CYS75
R	VAL78
R	HIS79
R	ALA474
R	PRO475
R	ARG476
R	LEU479
R	VAL497
R	PRO498
R	SER499
R	CSO543
R	CYS546
R	NI1551

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI R 1551

Chain	Residue
R	CYS72
R	CYS75
R	CSO543
R	CYS546
R	FCO1550

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG R 1553

Chain	Residue
R	GLU53
R	LEU495
R	HIS549
R	HOH2049
R	HOH2050
R	HOH2275

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL R 1561

Chain	Residue
B	ALA55
R	ASN181
R	ALA182
R	TYR183
R	LEU185
R	ARG529
R	HOH2389

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL R 1562

Chain	Residue
B	LEU137
R	GLY409
R	LYS410
R	HOH2336

site_id	DC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL R 1563

Chain	Residue
R	ARG100
R	ASN104
R	PHE295
R	ALA296
R	THR297
R	GLN310
R	GLU445
R	HOH2098
R	HOH2101
R	HOH2245

site_id	DC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO S 1550

Chain	Residue
S	CYS75
S	VAL78
S	HIS79
S	ALA474
S	PRO475
S	ARG476
S	LEU479
S	VAL497
S	PRO498
S	SER499
S	CSO543
S	CYS546
S	NI1551

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI S 1551

Chain	Residue
S	CYS72
S	CYS75
S	CSO543
S	CYS546
S	FCO1550

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG S 1553

Chain	Residue
S	GLU53
S	LEU495
S	HIS549
S	HOH2023
S	HOH2024
S	HOH2196

site_id	DC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL S 1561

Chain	Residue
S	ARG100
S	ASN104
S	PHE295
S	ALA296
S	THR297
S	GLU445
S	HOH2074
S	HOH2183
S	HOH2279

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
Q	ARG50-CYS75

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

Chain	Residue	Details
Q	PHE540-HIS549

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