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(-) Description

Title :  CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES WITH K362M MUTATION
 
Authors :  J. Liu, L. Qin, S. Ferguson-Miller
Date :  26 Aug 10  (Deposition) - 02 Feb 11  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transmembrane Protein Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, L. Qin, S. Ferguson-Miller
Crystallographic And Online Spectral Evidence For Role Of Conformational Change And Conserved Water In Cytochrome Oxidase Proton Pump.
Proc. Natl. Acad. Sci. Usa V. 108 1284 2011
PubMed-ID: 21205904  |  Reference-DOI: 10.1073/PNAS.1012846108

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE, AA3 TYPE, SUBUNIT I
    Chains: A, C
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRK415-1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 17-551
    Gene: COXI, CTAD, RHOS4_04590, RSP_1877
    Mutation: YES
    Organism Scientific: RHODOBACTER SPHAEROIDES 2.4.1
    Organism Taxid: 272943
    Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158
 
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: PRK415-1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-281
    Gene: COXII, CTAB, CTAC, RHOS4_04060, RSP_1826
    Organism Scientific: RHODOBACTER SPHAEROIDES 2.4.1
    Organism Taxid: 272943
    Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158

 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  (10, 41)

Asymmetric Unit (10, 41)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CD4Ligand/IonCADMIUM ION
4CU4Ligand/IonCOPPER (II) ION
3CU12Ligand/IonCOPPER (I) ION
5DMU11Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA4Ligand/IonHEME-A
7HTH1Ligand/Ion(2S,3R)-HEPTANE-1,2,3-TRIOL
8MG2Ligand/IonMAGNESIUM ION
9OH2Ligand/IonHYDROXIDE ION
10TRD9Ligand/IonTRIDECANE
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
4CU-1Ligand/IonCOPPER (II) ION
3CU11Ligand/IonCOPPER (I) ION
5DMU6Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA2Ligand/IonHEME-A
7HTH1Ligand/Ion(2S,3R)-HEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9OH-1Ligand/IonHYDROXIDE ION
10TRD6Ligand/IonTRIDECANE
Biological Unit 2 (4, 11)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
4CU-1Ligand/IonCOPPER (II) ION
3CU11Ligand/IonCOPPER (I) ION
5DMU5Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA2Ligand/IonHEME-A
7HTH-1Ligand/Ion(2S,3R)-HEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9OH-1Ligand/IonHYDROXIDE ION
10TRD3Ligand/IonTRIDECANE

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHEA A:2 , CU A:5 , HIS A:284 , VAL A:287 , HIS A:334 , HOH A:727 , HOH A:806BINDING SITE FOR RESIDUE OH A 706
02AC2SOFTWAREMET A:56 , ALA A:57 , GLN A:61 , PHE A:502 , TRD A:552 , HOH A:771BINDING SITE FOR RESIDUE DMU A 1005
03AC3SOFTWARELEU A:34 , MET A:443 , SER A:444 , HOH A:769BINDING SITE FOR RESIDUE DMU A 7
04AC4SOFTWAREPHE A:76 , SER A:79BINDING SITE FOR RESIDUE TRD A 1013
05AC5SOFTWARELEU A:34 , VAL A:45 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , MET A:107 , VAL A:111 , GLY A:171 , TRP A:172 , TYR A:414 , HIS A:421 , SER A:425 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , PHE A:508 , HOH A:720 , HOH A:722 , HOH A:780BINDING SITE FOR RESIDUE HEA A 1
06AC6SOFTWAREHOH A:15 , TRP A:172 , TRP A:280 , VAL A:287 , 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 , ILE A:399 , LEU A:401 , SER A:402 , ASP A:407 , HIS A:411 , VAL A:416 , HIS A:419 , PHE A:420 , VAL A:423 , MET A:424 , ARG A:481 , OH A:706 , HOH A:727 , HOH A:735 , HOH A:765 , ILE B:68BINDING SITE FOR RESIDUE HEA A 2
07AC7SOFTWARELEU A:80 , TRP A:81 , PRO A:82 , DMU A:1005BINDING SITE FOR RESIDUE TRD A 552
08AC8SOFTWAREARG A:476 , THR B:41BINDING SITE FOR RESIDUE TRD A 3
09AC9SOFTWAREHIS A:284 , HIS A:333 , HIS A:334 , OH A:706 , HOH A:727BINDING SITE FOR RESIDUE CU A 5
10BC1SOFTWAREHIS A:411 , ASP A:412 , GLU B:254 , HOH B:738 , HOH B:744 , HOH B:750BINDING SITE FOR RESIDUE MG A 6
11BC2SOFTWAREGLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:758 , HOH A:771BINDING SITE FOR RESIDUE CA A 553
12BC3SOFTWARETRP A:451 , PHE A:510 , GLY A:513 , TYR A:517 , DMU B:2 , HOH B:26 , GLN B:142 , TRP B:143 , PRO B:164 , HOH B:730 , HOH B:737BINDING SITE FOR RESIDUE DMU B 1
13BC4SOFTWARETRP A:451 , HOH A:835 , DMU B:1BINDING SITE FOR RESIDUE DMU B 2
14BC5SOFTWARETRP A:371 , LEU B:75 , HIS B:96 , ASN B:97 , SER D:173 , PRO D:174 , GLU D:177 , HOH D:356BINDING SITE FOR RESIDUE DMU B 3
15BC6SOFTWAREPHE B:124 , ASN B:125 , GLU B:128BINDING SITE FOR RESIDUE DMU B 6
16BC7SOFTWAREGLU B:152 , GLU B:153 , ALA B:276 , GLU B:280 , HIS B:283 , HOH B:496 , HOH B:715 , ALA D:276 , GLU D:280 , HIS D:283BINDING SITE FOR RESIDUE HTH B 286
17BC8SOFTWARECYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU1 B:288BINDING SITE FOR RESIDUE CU B 287
18BC9SOFTWAREHIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU B:287BINDING SITE FOR RESIDUE CU1 B 288
19CC1SOFTWAREGLU B:280 , HIS B:283 , HIS B:285 , GLU D:152BINDING SITE FOR RESIDUE CD B 8
20CC2SOFTWAREHIS B:96 , GLU B:101 , HOH B:714 , HOH B:801 , HOH B:802BINDING SITE FOR RESIDUE CD B 9
21CC3SOFTWAREHEA C:2 , HIS C:284 , VAL C:287 , HIS C:334 , CU C:553 , HOH C:556BINDING SITE FOR RESIDUE OH C 706
22CC4SOFTWAREALA C:57 , GLN C:61 , SER C:83 , VAL C:85 , PHE C:502 , TRD C:552 , HOH C:597BINDING SITE FOR RESIDUE DMU C 10
23CC5SOFTWARETRP C:451BINDING SITE FOR RESIDUE DMU C 5
24CC6SOFTWAREMET C:443BINDING SITE FOR RESIDUE DMU C 9
25CC7SOFTWAREHOH C:3 , LEU C:34 , GLY C:38 , THR C:48 , MET C:51 , ARG C:52 , TRP C:95 , ILE C:99 , HIS C:102 , MET C:106 , MET C:107 , VAL C:111 , GLY C:171 , TRP C:172 , TYR C:414 , HIS C:421 , MET C:424 , SER C:425 , VAL C:429 , MET C:460 , PHE C:468 , GLN C:471 , ARG C:481 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:554 , HOH C:606BINDING SITE FOR RESIDUE HEA C 1
26CC8SOFTWAREHOH C:15 , TRP C:172 , TRP C:280 , VAL C:287 , TYR C:288 , HIS C:333 , HIS C:334 , THR C:352 , ILE C:355 , THR C:359 , GLY C:360 , GLY C:395 , GLY C:398 , LEU C:401 , SER C:402 , ASP C:407 , HIS C:411 , VAL C:416 , HIS C:419 , PHE C:420 , VAL C:423 , MET C:424 , ARG C:481 , HOH C:556 , HOH C:565 , HOH C:593 , OH C:706BINDING SITE FOR RESIDUE HEA C 2
27CC9SOFTWAREDMU C:10 , LEU C:80 , TRP C:81 , PRO C:82BINDING SITE FOR RESIDUE TRD C 552
28DC1SOFTWAREHIS C:284 , HIS C:333 , HIS C:334 , HOH C:556 , OH C:706BINDING SITE FOR RESIDUE CU C 553
29DC2SOFTWAREHIS C:411 , ASP C:412 , HOH C:585 , GLU D:254 , HOH D:316 , HOH D:327BINDING SITE FOR RESIDUE MG C 6
30DC3SOFTWAREGLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:586 , HOH C:597BINDING SITE FOR RESIDUE CA C 7
31DC4SOFTWAREPRO D:121 , PHE D:124 , GLU D:128BINDING SITE FOR RESIDUE DMU D 4
32DC5SOFTWAREHIS D:96 , ASN D:97BINDING SITE FOR RESIDUE DMU D 8
33DC6SOFTWAREHIS C:472 , ARG C:476 , THR D:41BINDING SITE FOR RESIDUE TRD D 3
34DC7SOFTWAREMET C:353 , LEU D:112BINDING SITE FOR RESIDUE TRD D 14
35DC8SOFTWARECYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU1 D:287BINDING SITE FOR RESIDUE CU D 286
36DC9SOFTWAREHIS D:217 , CYS D:252 , CYS D:256 , MET D:263 , CU D:286BINDING SITE FOR RESIDUE CU1 D 287
37EC1SOFTWAREGLU B:152 , GLU D:280 , HIS D:283 , HIS D:285BINDING SITE FOR RESIDUE CD D 288
38EC2SOFTWAREHIS D:96 , GLU D:101 , HOH D:375 , HOH D:376BINDING SITE FOR RESIDUE CD D 9

(-) 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 3OMA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OMA)

(-) Exons   (0, 0)

(no "Exon" information available for 3OMA)

(-) 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:535
 aligned with Q3J5A7_RHOS4 | Q3J5A7 from UniProtKB/TrEMBL  Length:566

    Alignment length:535
                                    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     
         Q3J5A7_RHOS4    17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
               SCOP domains d3omaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee............hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oma A  17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIMIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
                                    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:256
 aligned with Q3J5G0_RHOS4 | Q3J5G0 from UniProtKB/TrEMBL  Length:303

    Alignment length:256
                                    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      
         Q3J5G0_RHOS4    30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGG 285
               SCOP domains d3omab1 B:30-129 automated matches                                                                  d3omab2 B:130-285 automated matches                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeee......eeee....hhhhh.....hhhhhhhhhhh..hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee........hhhhh.eeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oma B  30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHH 285
                                    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      


Chain C from PDB  Type:PROTEIN  Length:531
 aligned with Q3J5A7_RHOS4 | Q3J5A7 from UniProtKB/TrEMBL  Length:566

    Alignment length:531
                                    29        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       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549 
         Q3J5A7_RHOS4    20 WFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHT 550
               SCOP domains d3omac_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------COX1-3omaC01 C:26-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------COX1-3omaC02 C:26-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ---------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oma C  20 WFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIMIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHT 550
                                    29        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       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549 


Chain D from PDB  Type:PROTEIN  Length:256
 aligned with Q3J5G0_RHOS4 | Q3J5G0 from UniProtKB/TrEMBL  Length:303

    Alignment length:256
                                    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      
         Q3J5G0_RHOS4    30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGG 285
               SCOP domains d3omad1 D:30-129 automated matches                                                                  d3omad2 D:130-285 automated matches                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----COX2_TM-3omaD03 D:35-122                                                                -----------COX2-3omaD01 D:134-270                                                                                                                   --------------- Pfam domains (1)
           Pfam domains (2) -----COX2_TM-3omaD04 D:35-122                                                                -----------COX2-3omaD02 D:134-270                                                                                                                   --------------- Pfam domains (2)
         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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oma D  30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHH 285
                                    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
   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  (0, 0)

(no "CATH Domain" information available for 3OMA)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)
(-)
Clan: no clan defined [family: COX1] (19)
(-)
Clan: no clan defined [family: COX2_TM] (16)

(-) Gene Ontology  (17, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q3J5A7_RHOS4 | Q3J5A7)
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: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: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   (Q3J5G0_RHOS4 | Q3J5G0)
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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  3oma
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 Related Entries

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

UniProtKB/TrEMBL
        Q3J5A7_RHOS4 | Q3J5A7: 3om3 3omi 3omn
        Q3J5G0_RHOS4 | Q3J5G0: 3om3 3omi 3omn

(-) Related Entries Specified in the PDB File

2gsm THE WILD TYPE FORM OF THIS MUTANT
3om3 THE SAME KIND PROTEIN CRYSTAL REDUCED WITH SODIUM DITHIONITE
3omi
3omn