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(-) Description

Title :  CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES COMPLEXED WITH DEOXYCHOLIC ACID
 
Authors :  L. Qin, D. A. Mills, L. Buhrow, C. Hiser, S. Ferguson-Miller
Date :  15 Jul 08  (Deposition) - 16 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transmembrane Protein Complex, Deoxycholic Acid, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Qin, D. A. Mills, L. Buhrow, C. Hiser, S. Ferguson-Miller
A Conserved Steroid Binding Site In Cytochrome C Oxidase.
Biochemistry V. 47 9931 2008
PubMed-ID: 18759498  |  Reference-DOI: 10.1021/BI8013483
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE SUBUNIT 1
    Chains: A, C
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRK415
    Expression System Strain: DELTAIDELTAIV
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: CTAD
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 37DELTA4
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE I, CYTOCHROME AA3 SUBUNIT 1
 
Molecule 2 - CYTOCHROME C OXIDASE SUBUNIT 2
    Chains: B, D
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRK415
    Expression System Strain: DELTAIDELTAIV
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-281
    Gene: CTAC, COXII, CTAB
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 37DELTA4
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME AA3 SUBUNIT 2, OXIDASE AA(3) SUBUNIT 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 57)

Asymmetric Unit (11, 57)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CD5Ligand/IonCADMIUM ION
3CU6Ligand/IonCOPPER (II) ION
4DMU9Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
5DXC1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OICACID
6HEA4Ligand/IonHEME-A
7HTO1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG2Ligand/IonMAGNESIUM ION
9OH2Ligand/IonHYDROXIDE ION
10PO42Ligand/IonPHOSPHATE ION
11TRD23Ligand/IonTRIDECANE
Biological Unit 1 (5, 21)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
3CU-1Ligand/IonCOPPER (II) ION
4DMU6Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
5DXC-1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OICACID
6HEA2Ligand/IonHEME-A
7HTO1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9OH-1Ligand/IonHYDROXIDE ION
10PO41Ligand/IonPHOSPHATE ION
11TRD11Ligand/IonTRIDECANE
Biological Unit 2 (5, 19)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
3CU-1Ligand/IonCOPPER (II) ION
4DMU3Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
5DXC1Ligand/Ion(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OICACID
6HEA2Ligand/IonHEME-A
7HTO-1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9OH-1Ligand/IonHYDROXIDE ION
10PO41Ligand/IonPHOSPHATE ION
11TRD12Ligand/IonTRIDECANE

(-) Sites  (44, 44)

Asymmetric Unit (44, 44)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:83 , ALA A:84 , ASN A:87 , HOH A:1636 , TRP C:371 , LEU D:75 , PHE D:94 , HIS D:96 , ASN D:97BINDING SITE FOR RESIDUE DMU A 567
02AC2SOFTWARETRP A:20 , MET A:443 , LEU A:512 , HOH A:1560BINDING SITE FOR RESIDUE DMU A 1004
03AC3SOFTWAREMET A:56 , ALA A:57 , GLN A:61 , SER A:83 , PHE A:502 , PHE A:505 , HOH A:1563 , HOH A:1606BINDING SITE FOR RESIDUE DMU A 1005
04AC4SOFTWARETRP A:371 , HIS B:96 , ASN B:97BINDING SITE FOR RESIDUE DMU B 1003
05AC5SOFTWAREPRO B:121 , GLU B:128 , HOH B:1182BINDING SITE FOR RESIDUE DMU B 1011
06AC6SOFTWAREMET C:56 , GLN C:61 , PHE C:62 , SER C:83 , PHE C:505 , HOH C:642 , HOH C:684BINDING SITE FOR RESIDUE DMU C 567
07AC7SOFTWAREGLU A:86 , PRO B:174 , TYR C:318 , HOH C:718 , HOH C:752BINDING SITE FOR RESIDUE DMU C 568
08AC8SOFTWAREPRO D:121 , PHE D:124 , GLU D:128BINDING SITE FOR RESIDUE DMU D 11
09AC9SOFTWAREHIS A:284 , HIS A:333 , HIS A:334 , HOH A:1511BINDING SITE FOR RESIDUE CU A 1023
10BC1SOFTWAREHIS A:411 , ASP A:412 , GLU B:254 , HOH B:1064 , HOH B:1070 , HOH B:1077BINDING SITE FOR RESIDUE MG A 1006
11BC2SOFTWAREGLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:1550 , HOH A:1563BINDING SITE FOR RESIDUE CA A 1007
12BC3SOFTWAREHIS A:284 , HIS A:334 , HOH A:1511BINDING SITE FOR RESIDUE OH A 1501
13BC4SOFTWAREPHE A:135 , PRO A:136 , ARG A:137 , MET A:138BINDING SITE FOR RESIDUE PO4 A 1001
14BC5SOFTWARECYS B:252 , GLU B:254 , CYS B:256 , HIS B:260BINDING SITE FOR RESIDUE CU B 1022
15BC6SOFTWAREHIS B:217 , CYS B:252 , CYS B:256 , MET B:263BINDING SITE FOR RESIDUE CU B 1004
16BC7SOFTWAREGLU B:280 , HIS B:283 , HIS B:285 , GLU D:152BINDING SITE FOR RESIDUE CD B 1008
17BC8SOFTWAREHIS B:96 , GLU B:101 , HOH B:1157 , HOH B:1158BINDING SITE FOR RESIDUE CD B 1009
18BC9SOFTWAREHIS B:284 , HIS B:286 , HOH B:1162 , HOH B:1176BINDING SITE FOR RESIDUE CD B 1010
19CC1SOFTWAREHIS C:284 , HIS C:333 , HIS C:334BINDING SITE FOR RESIDUE CU C 569
20CC2SOFTWAREHIS C:411 , ASP C:412 , HOH C:628 , GLU D:254 , HOH D:321 , HOH D:333BINDING SITE FOR RESIDUE MG C 570
21CC3SOFTWAREGLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:629 , HOH C:642BINDING SITE FOR RESIDUE CA C 571
22CC4SOFTWAREHIS C:284 , HIS C:334 , HOH C:589BINDING SITE FOR RESIDUE OH C 572
23CC5SOFTWAREPHE C:135 , PRO C:136 , ARG C:137 , MET C:138BINDING SITE FOR RESIDUE PO4 C 573
24CC6SOFTWARECYS D:252 , GLU D:254 , CYS D:256 , HIS D:260BINDING SITE FOR RESIDUE CU D 3
25CC7SOFTWAREHIS D:217 , CYS D:252 , CYS D:256 , MET D:263BINDING SITE FOR RESIDUE CU D 4
26CC8SOFTWAREGLU B:152 , GLU D:280 , HIS D:283 , HIS D:285BINDING SITE FOR RESIDUE CD D 8
27CC9SOFTWAREHOH C:719 , HIS D:96 , GLU D:101BINDING SITE FOR RESIDUE CD D 9
28DC1SOFTWARELEU A:34 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , MET A:107 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , MET A:424 , SER A:425 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:1507 , HOH A:1509 , HOH A:1573BINDING SITE FOR RESIDUE HEA A 1502
29DC2SOFTWARETRP A:172 , TRP A:280 , TYR A:288 , HIS A:333 , HIS A:334 , THR A:352 , ILE A:355 , THR A:359 , GLY A:360 , GLY A:395 , GLY A:398 , LEU A:401 , SER A:402 , ASP A:407 , HIS A:411 , HIS A:419 , PHE A:420 , MET A:424 , ARG A:481 , HOH A:1511 , HOH A:1520 , HOH A:1527 , HOH A:1536 , HOH A:1556BINDING SITE FOR RESIDUE HEA A 1503
30DC3SOFTWARETRP A:451 , GLY A:513 , TYR A:517BINDING SITE FOR RESIDUE TRD A 1504
31DC4SOFTWARELEU A:80 , TRP A:81BINDING SITE FOR RESIDUE TRD A 1505
32DC5SOFTWAREARG A:476 , THR B:41 , GLY B:42BINDING SITE FOR RESIDUE TRD A 1506
33DC6SOFTWAREPHE A:76 , SER A:79BINDING SITE FOR RESIDUE TRD A 1013
34DC7SOFTWAREPHE B:71BINDING SITE FOR RESIDUE TRD B 1012
35DC8SOFTWAREALA B:276 , GLU B:280 , HIS B:283 , HOH B:1160 , HOH B:1178 , GLU D:152 , ALA D:276 , GLU D:280 , HIS D:283 , HOH D:298BINDING SITE FOR RESIDUE HTO B 1
36DC9SOFTWARELEU C:34 , THR C:48 , MET C:51 , ARG C:52 , TRP C:95 , ILE C:99 , HIS C:102 , MET C:106 , MET C:107 , GLY C:171 , TRP C:172 , TYR C:414 , PHE C:420 , HIS C:421 , MET C:424 , SER C:425 , PHE C:468 , GLN C:471 , ARG C:481 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:585 , HOH C:587 , HOH C:652BINDING SITE FOR RESIDUE HEA C 574
37EC1SOFTWARETRP C:172 , TRP C:280 , TYR C:288 , HIS C:333 , THR C:352 , ILE C:355 , THR C:359 , GLY C:360 , GLY C:395 , GLY C:398 , ILE C:399 , LEU C:401 , SER C:402 , ASP C:407 , HIS C:411 , HIS C:419 , PHE C:420 , MET C:424 , ARG C:481 , HOH C:589 , HOH C:598 , HOH C:605 , HOH C:614 , HOH C:635BINDING SITE FOR RESIDUE HEA C 575
38EC2SOFTWAREPRO C:315 , TYR C:318 , ALA C:319 , ALA C:322 , PRO C:358 , ILE C:361 , HOH C:718 , HOH C:720 , HOH C:721 , HIS D:96 , GLU D:101BINDING SITE FOR RESIDUE DXC C 576
39EC3SOFTWAREMET C:443 , SER C:444BINDING SITE FOR RESIDUE TRD C 577
40EC4SOFTWARETYR C:50 , PHE C:76BINDING SITE FOR RESIDUE TRD C 579
41EC5SOFTWAREHIS C:223 , LYS C:224 , ASP C:536BINDING SITE FOR RESIDUE TRD C 583
42EC6SOFTWAREHIS C:127 , HIS C:300 , ALA C:303 , THR C:304 , PHE C:438 , HIS C:534 , ALA C:535 , ASP C:536 , THR C:537 , GLU C:539 , TRP C:540 , HOH C:686 , HOH C:701BINDING SITE FOR RESIDUE TRD C 584
43EC7SOFTWAREARG C:476 , THR D:41 , GLY D:42 , THR D:69BINDING SITE FOR RESIDUE TRD D 7
44EC8SOFTWAREPHE D:71BINDING SITE FOR RESIDUE TRD D 12

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:64 -A:88
2C:64 -C:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:176 -Pro A:177
2Ser A:544 -Pro A:545
3Gln B:142 -Trp B:143
4Pro C:176 -Pro C:177
5Ser C:544 -Pro C:545
6Gln D:142 -Trp D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DTU)

(-) PROSITE Motifs  (5, 10)

Asymmetric Unit (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  2A:20-551
C:20-552
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  2B:35-130
D:35-130
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  2B:131-281
D:131-281
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  2B:215-263
D:215-263
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  2A:280-334
C:280-334
Biological Unit 1 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  1A:20-551
-
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  1B:35-130
-
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  1B:131-281
-
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  1B:215-263
-
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  1A:280-334
-
Biological Unit 2 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  1-
C:20-552
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  1-
D:35-130
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  1-
D:131-281
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  1-
D:215-263
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  1-
C:280-334

(-) Exons   (0, 0)

(no "Exon" information available for 3DTU)

(-) Sequences/Alignments

Asymmetric 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:539
 aligned with COX1_RHOSH | P33517 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:539
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542         
           COX1_RHOSH    13 RRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
               SCOP domains d3dtua_ A: Bacterial aa3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3dtuA00 A:13-551 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------COX1  PDB: A:20-551 UniProt: 20-558                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: A:280-334 UniProt: 280-334              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dtu A  13 RRGFFTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542         


Chain B from PDB  Type:PROTEIN  Length:259
 aligned with COX2_RHOSH | Q03736 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:259
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278         
           COX2_RHOSH    29 SLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGGTY 287
               SCOP domains d3dtub2 B:29-129 Bacterial aa3 type cytochrome c oxidase subunit II                                  d3dtub1 B:130-287 Cytochrome c oxidase                                                                                                                         SCOP domains
               CATH domains ------3dtuB01 B:35-130  [code=1.10.287.90, no name defined]                                           3dtuB02 B:131-283 Cupredoxins -  blue copper proteins                                                                                                    ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeee....eeeee....hhhhh.....hhhhhhhhhhh..hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee........hhhhh.eeeeeehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------COX2_TM  PDB: B:35-130 UniProt: 35-130                                                          COX2_CUA  PDB: B:131-281 UniProt: 131-281                                                                                                              ------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: B:215-263 UniProt: 215-263            ------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dtu B  29 SLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHHHH 287
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278         


Chain C from PDB  Type:PROTEIN  Length:536
 aligned with COX1_RHOSH | P33517 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:536
                                    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      
           COX1_RHOSH    17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFE 552
               SCOP domains d3dtuc_ C: Bacterial aa3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3dtuC00 C:17-552 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---COX1  PDB: C:20-552 UniProt: 20-558                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: C:280-334 UniProt: 280-334              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dtu C  17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFE 552
                                    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 D from PDB  Type:PROTEIN  Length:258
 aligned with COX2_RHOSH | Q03736 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:258
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277        
           COX2_RHOSH    28 QSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGG 285
               SCOP domains d3dtud2 D:28-129 Bacterial aa3 type cytochrome c oxidase subunit II                                   d3dtud1 D:130-285 Cytochrome c oxidase                                                                                                                       SCOP domains
               CATH domains -------3dtuD01 D:35-130  [code=1.10.287.90, no name defined]                                           3dtuD02 D:131-283 Cupredoxins -  blue copper proteins                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeee....eeeee....hhhhh.....hhhhhhhhhhh..hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee........hhhhh.eeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------COX2_TM  PDB: D:35-130 UniProt: 35-130                                                          COX2_CUA  PDB: D:131-281 UniProt: 131-281                                                                                                              ---- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: D:215-263 UniProt: 215-263            ---------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dtu D  28 QSLEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHH 285
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DTU)

(-) Gene Ontology  (19, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (COX1_RHOSH | P33517)
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,D   (COX2_RHOSH | Q03736)
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.

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  COX2_RHOSH | Q03736
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        COX1_RHOSH | P33517: 1m56 1m57 2gsm 3fye 3fyi
        COX2_RHOSH | Q03736: 1m56 1m57 2gsm 3fye 3fyi

(-) Related Entries Specified in the PDB File

2gsm CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RODOBACTER SPHAEROIDES WITHOUT DEOXYCHOLIC ACID