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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

Authors :   A. Harrenga, H. Michel

Date :   30 Aug 99 (Deposition) - 02 Dec 99 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,C,D,H,L

Keywords :   Oxidoreductase/Immune System, Complex (Oxidoreductase-Antibody), Electron Transport, Transmembrane, Cytochrome Oxidase, Antibody Complex, Oxidoreductase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Harrenga, H. Michel
The Cytochrome C Oxidase From Paracoccus Denitrificans Does Not Change The Metal Center Ligation Upon Reduction
J. Biol. Chem. V. 274 33296 1999
PubMed-ID: 10559205 | Reference-DOI: 10.1074/JBC.274.47.33296

Molecule 1 - CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA
	Atcc	:	13543
	Cellular Location	:	CYTOPLASMIC MEMBRANE
	Chains	:	A
	EC Number	:	1.9.3.1
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Synonym	:	CYTOCHROME AA3 SUBUNIT 1-BETA

Molecule 2 - CYTOCHROME C OXIDASE POLYPEPTIDE II
	Atcc	:	13543
	Cellular Location	:	CYTOPLASMIC MEMBRANE
	Chains	:	B
	EC Number	:	1.9.3.1
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Synonym	:	CYTOCHROME AA3 SUBUNIT 2, OXIDASE AA(3) SUBUNIT 2

Molecule 3 - CYTOCHROME C OXIDASE POLYPEPTIDE III
	Atcc	:	13543
	Cellular Location	:	CYTOPLASMIC MEMBRANE
	Chains	:	C
	EC Number	:	1.9.3.1
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Synonym	:	CYTOCHROME AA3SUBUNIT 3, OXIDASE AA(3) SUBUNIT 3

Molecule 4 - CCYTOCHROME C OXIDASE
	Atcc	:	13543
	Cellular Location	:	CYTOPLASMIC MEMBRANE
	Chains	:	D
	EC Number	:	1.9.3.1
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266
	Synonym	:	CYTOCHROME AA3

Molecule 5 - HEAVY CHAIN ANTIBODY FV FRAGMENT
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 6 - LIGHT CHAIN ANTIBODY FV FRAGMENT
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 8)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CU	1	Ligand/Ion	COPPER (II) ION
3	CUA	1	Ligand/Ion	DINUCLEAR COPPER ION
4	HEA	2	Ligand/Ion	HEME-A
5	MN	1	Ligand/Ion	MANGANESE (II) ION
6	PC1	2	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:276 , HIS A:325 , HIS A:326	BINDING SITE FOR RESIDUE CU Y 2
2	AC2	SOFTWARE	GLU A:56 , HIS A:59 , PRO A:60 , GLY A:61 , GLN A:63	BINDING SITE FOR RESIDUE CA Z 1
3	AC3	SOFTWARE	HIS A:403 , ASP A:404 , GLU B:218	BINDING SITE FOR RESIDUE MN Z 2
4	AC4	SOFTWARE	LEU A:36 , ALA A:39 , GLY A:40 , VAL A:47 , THR A:50 , ARG A:54 , TRP A:87 , ILE A:91 , HIS A:94 , MET A:98 , VAL A:103 , ALA A:106 , GLY A:163 , TRP A:164 , TYR A:406 , VAL A:409 , PHE A:412 , HIS A:413 , MET A:416 , SER A:417 , VAL A:421 , MET A:452 , ARG A:473 , ARG A:474 , TYR A:475 , PHE A:500	BINDING SITE FOR RESIDUE HEA X 1
5	AC5	SOFTWARE	TRP A:164 , VAL A:279 , TYR A:280 , HIS A:325 , HIS A:326 , ALA A:348 , THR A:351 , GLY A:387 , GLY A:390 , VAL A:391 , LEU A:393 , SER A:394 , ASP A:399 , HIS A:403 , VAL A:408 , HIS A:411 , PHE A:412 , VAL A:415 , ARG A:473 , ARG A:474 , VAL B:45 , ILE B:88	BINDING SITE FOR RESIDUE HEA X 2
6	AC6	SOFTWARE	HIS B:181 , CYS B:216 , GLU B:218 , CYS B:220 , HIS B:224 , MET B:227	BINDING SITE FOR RESIDUE CUA Y 1
7	AC7	SOFTWARE	LEU A:233 , TRP A:323 , GLN A:336 , TYR A:339 , ARG B:198 , VAL C:102 , TRP C:106 , LYS C:110 , TYR C:114 , PRO C:121 , ASP C:124 , SER D:37 , ASN D:48	BINDING SITE FOR RESIDUE PC1 P 2
8	AC8	SOFTWARE	LEU C:55 , TRP C:66 , VAL C:69 , VAL C:70 , GLY C:73 , GLU C:74 , HIS C:78 , LEU C:86 , PHE C:90 , ILE C:222 , ILE C:225 , PHE C:226 , VAL C:229 , ARG C:233 , GLN C:238 , THR C:240 , GLN C:243 , HIS C:244 , VAL C:245 , GLY C:246	BINDING SITE FOR RESIDUE PC1 P 3

Asymmetric/Biological Unit

No.	Residues
1	A:66	-	A:80
2	H:22	-	H:96
3	L:23	-	L:88

Asymmetric/Biological Unit

No.	Residues
1	Pro A:168	-	Pro A:169
2	Ser A:536	-	Pro A:537
3	Ser C:120	-	Pro C:121
4	Thr L:7	-	Pro L:8
5	Pro L:95	-	Pro L:96

(no "SAP(SNP)/Variant" information available for 1QLE)

Asymmetric/Biological Unit (6, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COX3	PS50253	Heme-copper oxidase subunit III family profile.	COX3_PARDE	5-274	1	C:4-273
2	COX1	PS50855	Cytochrome oxidase subunit I profile.	COX1B_PARDE	22-550	1	A:22-550
3	COX2_TM	PS50999	Cytochrome oxidase subunit II transmembrane region profile.	COX2_PARDE	41-136	1	B:12-107
4	COX2_CUA	PS50857	Cytochrome oxidase subunit II copper A binding domain profile.	COX2_PARDE	138-274	1	B:109-245
5	COX2	PS00078	CO II and nitrous oxide reductase dinuclear copper centers signature.	COX2_PARDE	208-256	1	B:179-227
6	COX1_CUB	PS00077	Heme-copper oxidase catalytic subunit, copper B binding region signature.	COX1B_PARDE	272-326	1	A:272-326

(no "Exon" information available for 1QLE)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:538
 aligned with COX1B_PARDE | P98002 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:538
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546        
          COX1B_PARDE    17 GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDR 554
               SCOP domains d1qlea_ A: Bacterial aa3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qleA00 A:17-554 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -----------COX1-1qleA01 A:28-496                                                                                                                                                                                                                                                                                                                                                                                                                                                                ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----COX1  PDB: A:22-550 UniProt: 22-550                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ---- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: A:272-326 UniProt: 272-326              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qle A  17 GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDR 554
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with COX2_PARDE | P08306 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:252
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  
           COX2_PARDE    30 QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAA 281
               SCOP domains d1qleb2 B:1-107 Bacterial aa3 type cytochrome c oxidase subunit II                                         d1qleb1 B:108-252 Cytochrome c oxidase                                                                                                            SCOP domains
               CATH domains 1qleB01 B:1-24,B:106-2521qleB02 B:25-105  [code=1.10.287.90, no name defined]                            1qleB01 B:1-24,B:106-252 Cupredoxins -  blue copper proteins                                                                                        CATH domains
               Pfam domains -----------COX2_TM-1qleB02 B:12-99                                                                 ------------COX2-1qleB01 B:112-234                                                                                                     ------------------ Pfam domains
     Sec.struct. author (1) hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------eeee----eee--------eeeee----eeeee-------eee-----eeeeee------------eeeeeee------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -----------COX2_TM  PDB: B:12-107 UniProt: 41-136                                                          -COX2_CUA  PDB: B:109-245 UniProt: 138-274                                                                                                ------- PROSITE (3)
                PROSITE (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: B:179-227 UniProt: 208-256            ------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qle B   1 QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAA 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain C from PDB  Type:PROTEIN  Length:273
 aligned with COX3_PARDE | P06030 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
           COX3_PARDE     2 AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR 274
               SCOP domains d1qlec_ C: Bacterial aa3 type cytochrome c oxidase subunit III                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qleC01 C:1-77  [code=1.10.287.70, no name defined]                          1qleC02 C:78-273  [code=1.20.120.80, no name defined]                                                                                                                                                CATH domains
               Pfam domains -----COX3-1qleC01 C:6-272                                                                                                                                                                                                                                                       - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---COX3  PDB: C:4-273 UniProt: 5-274                                                                                                                                                                                                                                              PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qle C   1 AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain D from PDB  Type:PROTEIN  Length:43
 aligned with COX4_PARDE | P77921 from UniProtKB/Swiss-Prot  Length:50

    Alignment length:43
                                    17        27        37        47   
           COX4_PARDE     8 TDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLALANS  50
               SCOP domains d1qled_ D:                                  SCOP domains
               CATH domains 1qleD00 D:7-49                              CATH domains
               Pfam domains --COX4_pro_2-1qleD01 D:9-49                 Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 1qle D   7 TDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLALANS  49
                                    16        26        36        46

Chain H from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d1qleh_ H: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1qleH00 H:1-119 Immunoglobulins                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee....eeeeeeee..hhhhh.eeeeeee....eeeeeee......eeehhhh....eeeee....eeeeee........eeee..eee...eeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1qle H   1 EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSA 119
                                    10        20        30        40        50        60        70        80        90       100       110

Chain L from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d1qlel_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                        SCOP domains
               CATH domains 1qleL00 L:1-108 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee........eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1qle L   1 DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIK 108
                                    10        20        30        40        50        60        70        80        90       100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (COX1B_PARDE | P98002)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009060	aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006119	oxidative phosphorylation	The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain B (COX2_PARDE | P08306)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain C (COX3_PARDE | P06030)

molecular function
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0015002	heme-copper terminal oxidase activity	Catalysis of the four-electron reduction of dioxygen (O2) to water, coupled to generation of a proton electrochemical gradient across a membrane.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0019646	aerobic electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to oxygen to generate a transmembrane electrochemical gradient.
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain D (COX4_PARDE | P77921)

molecular function
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	COX1B_PARDE \| P98002	:	1ar1 1zyy 3ehb 3hb3
	COX2_PARDE \| P08306	:	1ar1 1zyy 3ehb 3hb3

1ar1	STRUCTURE AT 2.7 ANGSTROM RESOLUTION OF THE PARACOCCUS DENITRIFICANS TWO-SUBUNIT CYTOCHROME C OXIDASE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (6, 6)

Exons (0, 0)

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SCOP Domains (7, 7)

CATH Domains (7, 8)

Pfam Domains (5, 5)

Gene Ontology (22, 47)

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Entries Sharing at Least One Protein Chain (UniProt ID)

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