Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3HB3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004129	molecular_function	cytochrome-c oxidase activity
A	0005886	cellular_component	plasma membrane
A	0006119	biological_process	oxidative phosphorylation
A	0006811	biological_process	monoatomic ion transport
A	0009060	biological_process	aerobic respiration
A	0015990	biological_process	electron transport coupled proton transport
A	0016020	cellular_component	membrane
A	0020037	molecular_function	heme binding
A	0045277	cellular_component	respiratory chain complex IV
A	0046872	molecular_function	metal ion binding
A	0070469	cellular_component	respirasome
A	1902600	biological_process	proton transmembrane transport
B	0004129	molecular_function	cytochrome-c oxidase activity
B	0005507	molecular_function	copper ion binding
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0022900	biological_process	electron transport chain
C	0002250	biological_process	adaptive immune response
C	0002376	biological_process	immune system process
C	0003823	molecular_function	antigen binding
C	0016064	biological_process	immunoglobulin mediated immune response
C	0019814	cellular_component	immunoglobulin complex
C	0072562	cellular_component	blood microparticle

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE HEA A 559

Chain	Residue
A	LEU36
A	VAL103
A	GLY163
A	TRP164
A	TYR406
A	PHE412
A	HIS413
A	MET416
A	SER417
A	ILE424
A	MET452
A	THR50
A	ILE459
A	PHE460
A	GLN463
A	ARG473
A	ARG474
A	TYR475
A	SER496
A	HOH584
A	HOH623
A	MET53
A	ARG54
A	TRP87
A	ILE91
A	HIS94
A	MET98
A	MET99

site_id	AC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE HEA A 560

Chain	Residue
A	TRP164
A	TRP272
A	VAL279
A	TYR280
A	HIS325
A	HIS326
A	THR351
A	GLY352
A	GLY387
A	GLY390
A	LEU393
A	SER394
A	ASP399
A	HIS403
A	VAL408
A	HIS411
A	PHE412
A	VAL415
A	MET416
A	ARG473
A	PEO576
A	HOH582
A	HOH583
A	HOH950
A	HOH959
B	VAL45
B	ILE88

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CU1 A 561

Chain	Residue
A	HIS276
A	HIS325
A	HIS326
A	PEO576

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 562

Chain	Residue
A	HIS403
A	ASP404
A	HOH578
B	GLU218
B	HOH285
B	HOH884

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 563

Chain	Residue
A	GLU56
A	HIS59
A	GLY61
A	GLN63
A	HOH851
A	HOH965

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LDA A 564

Chain	Residue
A	ASN457
A	PHE461
A	LMT572
B	LMT279

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LDA A 565

Chain	Residue
A	LEU72
A	ILE73
A	LDA567
A	LMT571

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE LDA A 566

Chain	Residue
A	GLN336

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LDA A 567

Chain	Residue
A	TYR52
A	ALA70
A	LEU72
A	LDA565

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT A 568

Chain	Residue
A	TRP443
A	LEU447
A	PHE502
A	LMT569
A	HOH779

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE LMT A 569

Chain	Residue
A	PRO441
A	TRP443
A	GLY505
A	TYR509
A	LMT568
D	VAL9

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE LMT A 570

Chain	Residue
A	LEU511
A	PRO537
A	LMT575
A	HOH964
A	ARG21
A	LYS29
A	LEU36
A	MET435

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE LMT A 571

Chain	Residue
A	GLN58
A	HIS59
A	GLN63
A	TYR64
A	ALA74
A	TYR494
A	PHE497
A	LDA565
A	LMT572
A	HOH593
A	HOH771
A	HOH787

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE LMT A 572

Chain	Residue
A	TYR484
A	ASN487
A	ILE488
A	ILE491
A	LDA564
A	LMT571
A	HOH787
A	HOH1306
A	HOH1325

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT A 573

Chain	Residue
A	ILE367
A	GLU368
A	PHE369
A	PHE377
B	ASN61
B	ARG62
B	ARG63

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LMT A 574

Chain	Residue
A	MET24
A	LEU130
A	LEU133

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE LMT A 575

Chain	Residue
A	TRP22
A	ARG438
A	LEU511
A	PHE512
A	ARG516
A	LMT570

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEO A 576

Chain	Residue
A	HIS276
A	HIS325
A	HIS326
A	HEA560
A	CU1561

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU1 B 270

Chain	Residue
B	CYS216
B	GLU218
B	CYS220
B	HIS224
B	CU1271

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CU1 B 271

Chain	Residue
B	HIS181
B	CYS216
B	CYS220
B	MET227
B	CU1270

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LDA B 272

Chain	Residue
A	THR389
A	HIS464
B	ASN19
B	LDA274

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LDA B 273

Chain	Residue
B	HIS36
B	PHE37
B	LDA276

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LDA B 274

Chain	Residue
B	TYR40
B	LDA272
B	HOH1291

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LDA B 275

Chain	Residue
B	ARG102
B	LMT278
B	LMT280

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE LDA B 276

Chain	Residue
B	HIS36
B	TYR40
B	LDA273

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE LMT B 278

Chain	Residue
B	PRO98
B	ARG102
B	GLU105
B	LDA275

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT B 279

Chain	Residue
A	PHE461
A	TYR484
A	TRP485
A	LDA564
B	ASN15
B	GLY16
B	MET18

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE LMT B 280

Chain	Residue
B	TRP33
B	LEU87
B	ILE99
B	LDA275
B	HOH1058
B	HOH1118
D	ASN28

site_id	DC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE LMT B 281

Chain	Residue
A	TRP363
B	LEU52
B	HIS73
B	ASN74
B	TRP81
B	GLU140
B	GLU142
B	LMT283

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE LMT B 282

Chain	Residue
A	LEU342
A	THR346
A	VAL349
B	VAL86
B	LEU89

site_id	DC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE LMT B 283

Chain	Residue
A	PHE356
B	PHE48
B	LEU51
B	LEU52
B	ILE55
B	ILE80
B	VAL84
B	LMT281
B	HOH1330

Functional Information from PROSITE/UniProt

site_id	PS00078
Number of Residues	49
Details	COX2 CO II and nitrous oxide reductase dinuclear copper centers signature. ViHawtipafavkqdavpgriaqlwfsvdqegvyfgq......CselCginHayM

Chain	Residue	Details
B	VAL179-MET227

site_id	PS00077
Number of Residues	55
Details	COX1_CUB Heme-copper oxidase catalytic subunit, copper B binding region signature. WFFGHPeVyiiilpgfgiishvistfakkpifgylpmvlamaaigilgfvvwa..HH

Chain	Residue	Details
A	TRP272-HIS326

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	170
Details	TOPO_DOM: Periplasmic

Chain	Residue	Details
B	GLN1-PRO26
B	MET106-ALA251
A	MET207-VAL217
A	LYS300-PHE303
A	GLY365-PHE369
A	ARG438-TYR440
A	LYS515-HIS558

site_id	SWS_FT_FI2
Number of Residues	62
Details	TRANSMEM: Helical

Chain	Residue	Details
B	LEU27-ARG59
B	THR75-GLU105

site_id	SWS_FT_FI3
Number of Residues	14
Details	TOPO_DOM: Cytoplasmic

Chain	Residue	Details
B	PHE60-ASN74
A	PRO152-GLY176
A	GLY252-GLY262
A	MET332
A	ALA396-ASP404
A	GLY470-TYR478

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING:

Chain	Residue	Details
B	HIS181
B	CYS216
B	GLU218
B	CYS220
B	HIS224
B	MET227

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Pyrrolidone carboxylic acid => ECO:0000269\|PubMed:2820725

Chain	Residue	Details
B	GLN1

site_id	SWS_FT_FI6
Number of Residues	29
Details	TRANSMEM: Helical; Name=IV

Chain	Residue	Details
A	TYR177-ASN206

site_id	SWS_FT_FI7
Number of Residues	33
Details	TRANSMEM: Helical; Name=V

Chain	Residue	Details
A	PRO218-PHE251

site_id	SWS_FT_FI8
Number of Residues	36
Details	TRANSMEM: Helical; Name=VI

Chain	Residue	Details
A	ASP263-LYS299

site_id	SWS_FT_FI9
Number of Residues	27
Details	TRANSMEM: Helical; Name=VII

Chain	Residue	Details
A	GLY304-GLY331

site_id	SWS_FT_FI10
Number of Residues	31
Details	TRANSMEM: Helical; Name=VIII

Chain	Residue	Details
A	SER333-GLY364

site_id	SWS_FT_FI11
Number of Residues	25
Details	TRANSMEM: Helical; Name=IX

Chain	Residue	Details
A	LYS370-GLN395

site_id	SWS_FT_FI12
Number of Residues	32
Details	TRANSMEM: Helical; Name=X

Chain	Residue	Details
A	THR405-GLY437

site_id	SWS_FT_FI13
Number of Residues	28
Details	TRANSMEM: Helical; Name=XI

Chain	Residue	Details
A	PRO441-GLN469

site_id	SWS_FT_FI14
Number of Residues	35
Details	TRANSMEM: Helical; Name=XII

Chain	Residue	Details
A	PRO479-GLY514

site_id	SWS_FT_FI15
Number of Residues	3
Details	BINDING: axial binding residue

Chain	Residue	Details
A	HIS94
A	HIS411
A	HIS413

site_id	SWS_FT_FI16
Number of Residues	4
Details	BINDING:

Chain	Residue	Details
A	HIS276
A	TYR280
A	HIS325
A	HIS326

site_id	SWS_FT_FI17
Number of Residues	2
Details	CROSSLNK: 1'-histidyl-3'-tyrosine (His-Tyr)

Chain	Residue	Details
A	HIS276
A	TYR280

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