eF-site ID 4whv-ABCDEFGHIJKL PDB Code 4whv Chain A, B, C, D, E, F, G, H, I, J, K, L click to enlarge Title E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Classification ligase/protein binding Compound Ubiquitin-conjugating enzyme E2 N Source Homo sapiens (Human) (UBB_HUMAN) Sequence A:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVL B:  LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQ DSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKL GRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLAN DVAEQWKTNEAQAIETARAWTRLYAMN C:  QEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQA QKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCS YCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMVNNL SSEVKERRIVLIRERK D:  PEFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEK MQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHS FCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKMV NNLSSEVKERRIVLIRERK E:  LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQ DSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKL GRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLAN DVAEQWKTNEAQAIETARAWTRLYAMN F:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVL G:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVL H:  LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQ DSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKL GRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLAN DVAEQWKTNEAQAIETARAWTRLYAMN I:  EKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCA HSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINK MVNNLSSEVKERRIVLIRERK J:  EKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCA HSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINK MVNNLSSEVKERRIVLIRERK K:  LPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQ DSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKL GRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLAN DVAEQWKTNEAQAIETARAWTRLYAMN L:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVL Description Functional site 1) chain C residue 418 type sequence C description binding site for residue ZN C 501 source : AC1 2) chain C residue 420 type sequence H description binding site for residue ZN C 501 source : AC1 3) chain C residue 437 type sequence C description binding site for residue ZN C 501 source : AC1 4) chain C residue 440 type sequence C description binding site for residue ZN C 501 source : AC1 5) chain C residue 403 type sequence C description binding site for residue ZN C 502 source : AC2 6) chain C residue 406 type sequence C description binding site for residue ZN C 502 source : AC2 7) chain C residue 423 type sequence C description binding site for residue ZN C 502 source : AC2 8) chain C residue 426 type sequence C description binding site for residue ZN C 502 source : AC2 9) chain D residue 418 type sequence C description binding site for residue ZN D 501 source : AC3 10) chain D residue 420 type sequence H description binding site for residue ZN D 501 source : AC3 11) chain D residue 437 type sequence C description binding site for residue ZN D 501 source : AC3 12) chain D residue 440 type sequence C description binding site for residue ZN D 501 source : AC3 13) chain D residue 403 type sequence C description binding site for residue ZN D 502 source : AC4 14) chain D residue 406 type sequence C description binding site for residue ZN D 502 source : AC4 15) chain D residue 423 type sequence C description binding site for residue ZN D 502 source : AC4 16) chain D residue 426 type sequence C description binding site for residue ZN D 502 source : AC4 17) chain I residue 418 type sequence C description binding site for residue ZN I 501 source : AC5 18) chain I residue 420 type sequence H description binding site for residue ZN I 501 source : AC5 19) chain I residue 437 type sequence C description binding site for residue ZN I 501 source : AC5 20) chain I residue 440 type sequence C description binding site for residue ZN I 501 source : AC5 21) chain I residue 403 type sequence C description binding site for residue ZN I 502 source : AC6 22) chain I residue 406 type sequence C description binding site for residue ZN I 502 source : AC6 23) chain I residue 423 type sequence C description binding site for residue ZN I 502 source : AC6 24) chain I residue 426 type sequence C description binding site for residue ZN I 502 source : AC6 25) chain J residue 418 type sequence C description binding site for residue ZN J 501 source : AC7 26) chain J residue 420 type sequence H description binding site for residue ZN J 501 source : AC7 27) chain J residue 437 type sequence C description binding site for residue ZN J 501 source : AC7 28) chain J residue 440 type sequence C description binding site for residue ZN J 501 source : AC7 29) chain J residue 403 type sequence C description binding site for residue ZN J 502 source : AC8 30) chain J residue 406 type sequence C description binding site for residue ZN J 502 source : AC8 31) chain J residue 423 type sequence C description binding site for residue ZN J 502 source : AC8 32) chain J residue 426 type sequence C description binding site for residue ZN J 502 source : AC8 33) chain E residue 27 type sequence P description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 34) chain E residue 28 type sequence D description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 35) chain E residue 31 type sequence N description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 36) chain E residue 31 type sequence N description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 37) chain E residue 32 type sequence A description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 38) chain E residue 33 type sequence R description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 39) chain E residue 35 type sequence F description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 40) chain E residue 36 type sequence H description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 41) chain E residue 55 type sequence E description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 42) chain E residue 56 type sequence L description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 43) chain E residue 73 type sequence T description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 44) chain E residue 75 type sequence I description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 45) chain E residue 143 type sequence W description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 46) chain E residue 147 type sequence Y description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 47) chain E residue 147 type sequence Y description binding site for Di-peptide TYR E 34 and LYS E 74 source : AC9 48) chain A residue 27-52 type prosite sequence KAKIQDKEGIPPDQQRLIFAGKQLED description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD source prosite : PS00299 49) chain C residue 418-427 type prosite sequence CAHSFCSYCI description ZF_RING_1 Zinc finger RING-type signature. CaHsFCsyCI source prosite : PS00518 50) chain A residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 51) chain F residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 52) chain G residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 53) chain L residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 54) chain A residue 29 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 source Swiss-Prot : SWS_FT_FI10 55) chain F residue 29 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 source Swiss-Prot : SWS_FT_FI10 56) chain G residue 29 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 source Swiss-Prot : SWS_FT_FI10 57) chain L residue 29 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 source Swiss-Prot : SWS_FT_FI10 58) chain A residue 33 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 source Swiss-Prot : SWS_FT_FI11 59) chain F residue 33 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 source Swiss-Prot : SWS_FT_FI11 60) chain G residue 33 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 source Swiss-Prot : SWS_FT_FI11 61) chain L residue 33 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 source Swiss-Prot : SWS_FT_FI11 62) chain A residue 63 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 63) chain F residue 63 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 64) chain G residue 63 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 65) chain L residue 63 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 66) chain A residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 67) chain F residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 68) chain G residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 69) chain L residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 70) chain A residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 71) chain F residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 72) chain G residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 73) chain L residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 74) chain H residue 92 type MOD_RES sequence K description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 75) chain K residue 92 type MOD_RES sequence K description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 76) chain A residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 77) chain F residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 78) chain G residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 79) chain L residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 80) chain A residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 81) chain F residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 82) chain G residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 83) chain L residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 84) chain A residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 85) chain A residue 48 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 86) chain F residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 87) chain F residue 48 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 88) chain G residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 89) chain G residue 48 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 90) chain L residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 91) chain L residue 48 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 92) chain A residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 93) chain F residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 94) chain G residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 95) chain L residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9

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