Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3W7R

Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004151	molecular_function	dihydroorotase activity
A	0004152	molecular_function	dihydroorotate dehydrogenase activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005743	cellular_component	mitochondrial inner membrane
A	0005829	cellular_component	cytosol
A	0006207	biological_process	'de novo' pyrimidine nucleobase biosynthetic process
A	0006221	biological_process	pyrimidine nucleotide biosynthetic process
A	0006225	biological_process	UDP biosynthetic process
A	0009220	biological_process	pyrimidine ribonucleotide biosynthetic process
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0016627	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors
A	0044205	biological_process	'de novo' UMP biosynthetic process
A	0106430	molecular_function	dihydroorotate dehydrogenase (quinone) activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 401

Chain	Residue
A	GLN165
A	HIS248
A	ARG298
A	SER299

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DDQ A 402

Chain	Residue
A	HIS41
A	THR45

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE DDQ A 403

Chain	Residue
A	DDQ404

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DDQ A 404

Chain	Residue
A	LEU49
A	DDQ403
A	HOH659
A	GLN47
A	GLY48

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE DDQ A 405

Chain	Residue
A	PHE62

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DDQ A 406

Chain	Residue
A	GLY33
A	PHE37
A	GLU40
A	HIS41

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE DDQ A 407

Chain	Residue
A	LEU68
A	W7A408
A	HOH772

site_id	AC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE W7A A 408

Chain	Residue
A	MET43
A	GLN47
A	PRO52
A	ALA55
A	HIS56
A	ALA59
A	LEU67
A	LEU68
A	PHE98
A	VAL134
A	ARG136
A	TYR356
A	THR360
A	PRO364
A	DDQ407
A	FMN409
A	HOH691

site_id	AC9
Number of Residues	26
Details	BINDING SITE FOR RESIDUE FMN A 409

Chain	Residue
A	ALA95
A	ALA96
A	GLY97
A	LYS100
A	GLY119
A	SER120
A	ASN145
A	ASN181
A	ASN212
A	LYS255
A	THR283
A	ASN284
A	THR285
A	SER305
A	GLY306
A	LEU309
A	VAL333
A	GLY334
A	GLY335
A	LEU355
A	TYR356
A	THR357
A	W7A408
A	ORO432
A	HOH503
A	HOH529

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 410

Chain	Residue
A	LYS307
A	THR314
A	GLN315
A	ARG318
A	GLU344
A	HOH524
A	HOH557
A	HOH779

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 411

Chain	Residue
A	HIS159
A	ALA322
A	GLN325
A	HIS394
A	HOH537
A	HOH574
A	HOH617

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 412

Chain	Residue
A	SER223
A	ASP264
A	HOH674

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 413

Chain	Residue
A	ARG57
A	HIS101
A	ASN150
A	HIS152
A	GOL416
A	HOH541
A	HOH645
A	HOH731

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 414

Chain	Residue
A	ARG61
A	SER64
A	GLU103
A	ACT439
A	HOH668
A	HOH762

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 415

Chain	Residue
A	ALA219
A	GLY220
A	ARG222
A	HOH791

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 416

Chain	Residue
A	GLN126
A	GLU127
A	SER151
A	HIS152
A	GOL413
A	HOH535
A	HOH701

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 417

Chain	Residue
A	GLU139
A	SER155
A	GLU158
A	HIS159
A	ARG162
A	GLN294
A	ALA296
A	GOL424
A	HOH754

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 418

Chain	Residue
A	ARG136
A	PRO138
A	HOH575
A	HOH732
A	HOH776

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 419

Chain	Residue
A	ARG241
A	ARG249
A	PRO250
A	ALA251
A	ASP278
A	GOL420
A	HOH609
A	HOH738
A	HOH796
A	HOH797

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 420

Chain	Residue
A	HIS86
A	ASP207
A	ARG246
A	VAL247
A	ARG249
A	GOL419
A	ACT438
A	HOH783

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 421

Chain	Residue
A	HIS86
A	LYS87
A	THR172
A	GLU173
A	HOH804

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 422

Chain	Residue
A	PRO52
A	PRO132
A	VAL134
A	PHE135
A	ARG200
A	HOH562
A	HOH659

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 423

Chain	Residue
A	MET30
A	THR32
A	GLY33
A	ARG72
A	HOH771

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 424

Chain	Residue
A	LYS124
A	SER155
A	GLU197
A	GOL417
A	ACT437
A	HOH776

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 425

Chain	Residue
A	PRO69
A	ALA71
A	MET111
A	PRO364
A	PRO365
A	GLY368
A	HOH712

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 426

Chain	Residue
A	GLU80
A	ARG82
A	THR387
A	HOH673

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 427

Chain	Residue
A	VAL272
A	LYS273
A	GLY276
A	ILE277
A	VAL328

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 428

Chain	Residue
A	LYS227
A	ARG231
A	HOH790

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 429

Chain	Residue
A	LYS170
A	THR261
A	GLN263
A	HOH553

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 430

Chain	Residue
A	MET30
A	ARG372
A	GLU373
A	ALA376
A	HOH611
A	HOH675

site_id	DC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 431

Chain	Residue
A	GLN141
A	LYS307
A	SER337
A	ARG347
A	TRP362
A	LYS369
A	GLN381
A	HOH540
A	HOH608
A	HOH639

site_id	DC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ORO A 432

Chain	Residue
A	LYS100
A	ASN145
A	TYR147
A	GLY148
A	PHE149
A	ASN212
A	SER215
A	ASN217
A	ASN284
A	THR285
A	FMN409

site_id	DC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 433

Chain	Residue
A	ARG245
A	HIS248
A	HOH723

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 434

Chain	Residue
A	ARG160
A	GLN325
A	ACT439
A	HOH762

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 435

Chain	Residue
A	ARG82
A	VAL83
A	LEU84
A	GLY85
A	ACT442
A	HOH570

site_id	DC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 A 436

Chain	Residue
A	ARG249

site_id	EC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 437

Chain	Residue
A	GOL424
A	HOH516

site_id	EC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT A 438

Chain	Residue
A	GLN168
A	ALA169
A	THR172
A	LEU205
A	ASP207
A	GOL420
A	HOH522
A	HOH600

site_id	EC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACT A 439

Chain	Residue
A	GLU103
A	ARG160
A	GOL414
A	SO4434
A	HOH565
A	HOH583
A	HOH799

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT A 440

Chain	Residue
A	SER64
A	GLY66
A	GLY107
A	HOH679
A	HOH802

site_id	EC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT A 441

Chain	Residue
A	HOH547

site_id	EC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 442

Chain	Residue
A	GLY85
A	HIS86
A	SO4435

site_id	EC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 443

Chain	Residue
A	GLU229
A	ARG232

Functional Information from PROSITE/UniProt

site_id	PS00911
Number of Residues	20
Details	DHODEHASE_1 Dihydroorotate dehydrogenase signature 1. GfveiGSVTpkpQeGNprPR

Chain	Residue	Details
A	GLY114-ARG133

site_id	PS00912
Number of Residues	21
Details	DHODEHASE_2 Dihydroorotate dehydrogenase signature 2. IIGvGGVsSgqdAleKIrAGA

Chain	Residue	Details
A	ILE330-ALA350

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	364
Details	TOPO_DOM: Mitochondrial intermembrane => ECO:0000250

Chain	Residue	Details
A	THR32-ARG396

site_id	SWS_FT_FI2
Number of Residues	1
Details	ACT_SITE: Nucleophile

Chain	Residue	Details
A	SER215

site_id	SWS_FT_FI3
Number of Residues	9
Details	BINDING: BINDING => ECO:0000269\|PubMed:10673429, ECO:0000269\|PubMed:16480261

Chain	Residue	Details
A	ALA96
A	SER120
A	ASN181
A	ASN212
A	LYS255
A	THR283
A	GLY306
A	GLY335
A	TYR356

site_id	SWS_FT_FI4
Number of Residues	3
Details	BINDING:

Chain	Residue	Details
A	LYS100
A	ASN145
A	ASN284

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	7
Details	M-CSA 109

Chain	Residue	Details
A	ASN145	electrostatic stabiliser
A	PHE149	activator, electrostatic stabiliser, enhance reactivity, polar/non-polar interaction
A	SER215	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar/non-polar interaction, proton acceptor, proton donor, proton relay
A	ASN217	electrostatic stabiliser
A	THR218	activator, electrostatic stabiliser, enhance reactivity, hydrogen bond acceptor
A	LYS255	electrostatic stabiliser, hydrogen bond donor
A	ASN284	electrostatic stabiliser

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