eF-site ID 1qle-ABCDHL PDB Code 1qle Chain A, B, C, D, H, L click to enlarge Title CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT Classification OXIDOREDUCTASE/IMMUNE SYSTEM Compound CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA Source ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; Sequence A:  GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRME LQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGV LMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYW MYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAG YSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFK VPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFF DPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVIST FAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQ QAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWA FGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVM SLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGS NLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYIS FASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPS PPPEHTFETLPKREDWDR B:  QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLY IITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVI WTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQ WYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDN PVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIA QLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYE AWLAGAKEEFAA C:  AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITF FGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTP VVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDS PIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHH AFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGL ADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMT QKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR D:  TDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLAL ANS H:  EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQT PEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLY LQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSA L:  DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQ GKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLP EDFGSYYCQHHYGTPPLTFGGGTKLEIK Description Functional site 1) chain A residue 276 type sequence H description BINDING SITE FOR RESIDUE CU Y 2 source : AC1 2) chain A residue 325 type sequence H description BINDING SITE FOR RESIDUE CU Y 2 source : AC1 3) chain A residue 326 type sequence H description BINDING SITE FOR RESIDUE CU Y 2 source : AC1 4) chain A residue 56 type sequence E description BINDING SITE FOR RESIDUE CA Z 1 source : AC2 5) chain A residue 59 type sequence H description BINDING SITE FOR RESIDUE CA Z 1 source : AC2 6) chain A residue 60 type sequence P description BINDING SITE FOR RESIDUE CA Z 1 source : AC2 7) chain A residue 61 type sequence G description BINDING SITE FOR RESIDUE CA Z 1 source : AC2 8) chain A residue 63 type sequence Q description BINDING SITE FOR RESIDUE CA Z 1 source : AC2 9) chain A residue 403 type sequence H description BINDING SITE FOR RESIDUE MN Z 2 source : AC3 10) chain A residue 404 type sequence D description BINDING SITE FOR RESIDUE MN Z 2 source : AC3 11) chain B residue 218 type sequence E description BINDING SITE FOR RESIDUE MN Z 2 source : AC3 12) chain A residue 36 type sequence L description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 13) chain A residue 39 type sequence A description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 14) chain A residue 40 type sequence G description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 15) chain A residue 47 type sequence V description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 16) chain A residue 50 type sequence T description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 17) chain A residue 54 type sequence R description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 18) chain A residue 87 type sequence W description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 19) chain A residue 91 type sequence I description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 20) chain A residue 94 type sequence H description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 21) chain A residue 98 type sequence M description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 22) chain A residue 103 type sequence V description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 23) chain A residue 106 type sequence A description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 24) chain A residue 163 type sequence G description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 25) chain A residue 164 type sequence W description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 26) chain A residue 406 type sequence Y description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 27) chain A residue 409 type sequence V description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 28) chain A residue 412 type sequence F description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 29) chain A residue 413 type sequence H description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 30) chain A residue 416 type sequence M description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 31) chain A residue 417 type sequence S description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 32) chain A residue 421 type sequence V description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 33) chain A residue 452 type sequence M description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 34) chain A residue 473 type sequence R description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 35) chain A residue 474 type sequence R description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 36) chain A residue 475 type sequence Y description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 37) chain A residue 500 type sequence F description BINDING SITE FOR RESIDUE HEA X 1 source : AC4 38) chain A residue 164 type sequence W description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 39) chain A residue 279 type sequence V description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 40) chain A residue 280 type sequence Y description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 41) chain A residue 325 type sequence H description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 42) chain A residue 326 type sequence H description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 43) chain A residue 348 type sequence A description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 44) chain A residue 351 type sequence T description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 45) chain A residue 387 type sequence G description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 46) chain A residue 390 type sequence G description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 47) chain A residue 391 type sequence V description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 48) chain A residue 393 type sequence L description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 49) chain A residue 394 type sequence S description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 50) chain A residue 399 type sequence D description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 51) chain A residue 403 type sequence H description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 52) chain A residue 408 type sequence V description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 53) chain A residue 411 type sequence H description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 54) chain A residue 412 type sequence F description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 55) chain A residue 415 type sequence V description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 56) chain A residue 473 type sequence R description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 57) chain A residue 474 type sequence R description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 58) chain B residue 45 type sequence V description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 59) chain B residue 88 type sequence I description BINDING SITE FOR RESIDUE HEA X 2 source : AC5 60) chain B residue 181 type sequence H description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 61) chain B residue 216 type sequence C description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 62) chain B residue 218 type sequence E description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 63) chain B residue 220 type sequence C description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 64) chain B residue 224 type sequence H description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 65) chain B residue 227 type sequence M description BINDING SITE FOR RESIDUE CUA Y 1 source : AC6 66) chain A residue 233 type sequence L description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 67) chain A residue 323 type sequence W description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 68) chain A residue 336 type sequence Q description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 69) chain A residue 339 type sequence Y description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 70) chain B residue 198 type sequence R description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 71) chain C residue 102 type sequence V description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 72) chain C residue 106 type sequence W description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 73) chain C residue 110 type sequence K description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 74) chain C residue 114 type sequence Y description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 75) chain C residue 121 type sequence P description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 76) chain C residue 124 type sequence D description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 77) chain D residue 37 type sequence S description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 78) chain D residue 48 type sequence N description BINDING SITE FOR RESIDUE PC1 P 2 source : AC7 79) chain C residue 55 type sequence L description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 80) chain C residue 66 type sequence W description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 81) chain C residue 69 type sequence V description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 82) chain C residue 70 type sequence V description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 83) chain C residue 73 type sequence G description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 84) chain C residue 74 type sequence E description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 85) chain C residue 78 type sequence H description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 86) chain C residue 86 type sequence L description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 87) chain C residue 90 type sequence F description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 88) chain C residue 222 type sequence I description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 89) chain C residue 225 type sequence I description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 90) chain C residue 226 type sequence F description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 91) chain C residue 229 type sequence V description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 92) chain C residue 233 type sequence R description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 93) chain C residue 238 type sequence Q description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 94) chain C residue 240 type sequence T description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 95) chain C residue 243 type sequence Q description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 96) chain C residue 244 type sequence H description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 97) chain C residue 245 type sequence V description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 98) chain C residue 246 type sequence G description BINDING SITE FOR RESIDUE PC1 P 3 source : AC8 99) chain D residue 17-48 type TRANSMEM sequence RHQQATFAGFIKGATWVSILSIAVLVFLALAN description Helical source Swiss-Prot : SWS_FT_FI1 100) chain C residue 78-79 type TRANSMEM sequence HT description Helical source Swiss-Prot : SWS_FT_FI1 101) chain C residue 167-168 type TRANSMEM sequence DR description Helical source Swiss-Prot : SWS_FT_FI1 102) chain C residue 238-244 type TRANSMEM sequence QMTQKQH description Helical source Swiss-Prot : SWS_FT_FI1 103) chain A residue 333-364 type TRANSMEM sequence SLTQQAYFMLATMTIAVPTGIKVFSWIATMWG description Helical; Name=VIII source Swiss-Prot : SWS_FT_FI10 104) chain A residue 370-395 type TRANSMEM sequence KTPMLWAFGFLFLFTVGGVTGVVLSQ description Helical; Name=IX source Swiss-Prot : SWS_FT_FI11 105) chain A residue 405-437 type TRANSMEM sequence TYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSG description Helical; Name=X source Swiss-Prot : SWS_FT_FI12 106) chain A residue 441-469 type TRANSMEM sequence PEWAGQLHFWMMFIGSNLIFFPQHFLGRQ description Helical; Name=XI source Swiss-Prot : SWS_FT_FI13 107) chain A residue 272-326 type prosite sequence WFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLA MAAIGILGFVVWAHH description COX1_CUB Heme-copper oxidase catalytic subunit, copper B binding region signature. WFFGHPeVyiiilpgfgiishvistfakkpifgylpmvlamaaigilgfvvwa..HH source prosite : PS00077 108) chain B residue 179-227 type prosite sequence VIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSE LCGINHAYM description COX2 CO II and nitrous oxide reductase dinuclear copper centers signature. ViHawtipafavkqdavpgriaqlwfsvdqegvyfgq......CselCginHayM source prosite : PS00078 109) chain A residue 94 type BINDING sequence H description axial binding residue source Swiss-Prot : SWS_FT_FI15 110) chain A residue 411 type BINDING sequence H description axial binding residue source Swiss-Prot : SWS_FT_FI15 111) chain A residue 413 type BINDING sequence H description axial binding residue source Swiss-Prot : SWS_FT_FI15 112) chain A residue 276 type BINDING sequence H description source Swiss-Prot : SWS_FT_FI16 113) chain A residue 280 type BINDING sequence Y description source Swiss-Prot : SWS_FT_FI16 114) chain A residue 325 type BINDING sequence H description source Swiss-Prot : SWS_FT_FI16 115) chain A residue 326 type BINDING sequence H description source Swiss-Prot : SWS_FT_FI16 116) chain A residue 276 type CROSSLNK sequence H description 1'-histidyl-3'-tyrosine (His-Tyr) source Swiss-Prot : SWS_FT_FI17 117) chain A residue 280 type CROSSLNK sequence Y description 1'-histidyl-3'-tyrosine (His-Tyr) source Swiss-Prot : SWS_FT_FI17 118) chain A residue 479-514 type TRANSMEM sequence PVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAG description Helical; Name=XII source Swiss-Prot : SWS_FT_FI14 119) chain D residue 49 type TOPO_DOM sequence S description Periplasmic source Swiss-Prot : SWS_FT_FI2 120) chain C residue 49-77 type TOPO_DOM sequence WMFLIGLVGVLYVMFGWWADVVNEGETGE description Periplasmic source Swiss-Prot : SWS_FT_FI2 121) chain C residue 80-115 type TOPO_DOM sequence PVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYP description Periplasmic source Swiss-Prot : SWS_FT_FI2 122) chain C residue 140-166 type TOPO_DOM sequence LPLINTLILLLSGVAVTWAHHAFVLEG description Periplasmic source Swiss-Prot : SWS_FT_FI2 123) chain C residue 169-197 type TOPO_DOM sequence KTTINGLIVAVILGVCFTGLQAYEYSHAA description Periplasmic source Swiss-Prot : SWS_FT_FI2 124) chain C residue 204-237 type TOPO_DOM sequence VYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKG description Periplasmic source Swiss-Prot : SWS_FT_FI2 125) chain C residue 37-48 type TOPO_DOM sequence GITFFGLPVEGP description Periplasmic source Swiss-Prot : SWS_FT_FI3 126) chain C residue 116-139 type TOPO_DOM sequence MGPDSPIKDGVWPPEGIVTFDPWH description Periplasmic source Swiss-Prot : SWS_FT_FI3 127) chain C residue 198-203 type TOPO_DOM sequence FGLADT description Periplasmic source Swiss-Prot : SWS_FT_FI3 128) chain A residue 263-299 type TRANSMEM sequence DPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAK description Helical; Name=VI source Swiss-Prot : SWS_FT_FI8 129) chain A residue 304-331 type TRANSMEM sequence GYLPMVLAMAAIGILGFVVWAHHMYTAG description Helical; Name=VII source Swiss-Prot : SWS_FT_FI9 130) chain B residue 181 type BINDING sequence H description source Swiss-Prot : SWS_FT_FI4 131) chain B residue 216 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI4 132) chain B residue 218 type BINDING sequence E description source Swiss-Prot : SWS_FT_FI4 133) chain B residue 220 type BINDING sequence C description source Swiss-Prot : SWS_FT_FI4 134) chain B residue 224 type BINDING sequence H description source Swiss-Prot : SWS_FT_FI4 135) chain B residue 227 type BINDING sequence M description source Swiss-Prot : SWS_FT_FI4 136) chain B residue 1 type MOD_RES sequence Q description Pyrrolidone carboxylic acid => ECO:0000269|PubMed:2820725 source Swiss-Prot : SWS_FT_FI5 137) chain A residue 177-206 type TRANSMEM sequence YSMDLAIFAVHVSGASSILGAINIITTFLN description Helical; Name=IV source Swiss-Prot : SWS_FT_FI6 138) chain A residue 218-251 type TRANSMEM sequence PLFAWSVFITAWLILLSLPVLAGAITMLLMDRNF description Helical; Name=V source Swiss-Prot : SWS_FT_FI7

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