eF-site ID 4rf0-AB PDB Code 4rf0 Chain A, B click to enlarge Title Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522) Classification PROTEIN BINDING Compound ORF1ab protein Source Human betacoronavirus 2c Jordan-N3/2012 (RL40_HUMAN) Sequence A:  TIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISD TIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHR FYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTLDL LKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGA PDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQ GLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHTTP WLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHA RLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSD B:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG Description (1)  ORF1ab protein, Ubiquitin-60S ribosomal protein L40 Functional site 1) chain A residue 1672 type sequence C description BINDING SITE FOR RESIDUE ZN A 1901 source : AC1 2) chain A residue 1675 type sequence C description BINDING SITE FOR RESIDUE ZN A 1901 source : AC1 3) chain A residue 1707 type sequence C description BINDING SITE FOR RESIDUE ZN A 1901 source : AC1 4) chain A residue 1709 type sequence C description BINDING SITE FOR RESIDUE ZN A 1901 source : AC1 5) chain A residue 1673 type sequence N description BINDING SITE FOR RESIDUE SO4 A 1902 source : AC2 6) chain A residue 1714 type sequence H description BINDING SITE FOR RESIDUE SO4 A 1902 source : AC2 7) chain A residue 1759 type sequence H description BINDING SITE FOR RESIDUE SO4 A 1902 source : AC2 8) chain A residue 1751 type sequence Q description BINDING SITE FOR RESIDUE SO4 A 1903 source : AC3 9) chain A residue 1752 type sequence G description BINDING SITE FOR RESIDUE SO4 A 1903 source : AC3 10) chain A residue 1787 type sequence K description BINDING SITE FOR RESIDUE SO4 A 1903 source : AC3 11) chain A residue 1659 type sequence E description BINDING SITE FOR RESIDUE SO4 A 1904 source : AC4 12) chain A residue 1660 type sequence L description BINDING SITE FOR RESIDUE SO4 A 1904 source : AC4 13) chain A residue 1684 type sequence G description BINDING SITE FOR RESIDUE SO4 A 1904 source : AC4 14) chain A residue 1685 type sequence L description BINDING SITE FOR RESIDUE SO4 A 1904 source : AC4 15) chain A residue 1686 type sequence K description BINDING SITE FOR RESIDUE SO4 A 1904 source : AC4 16) chain A residue 1668 type sequence W description BINDING SITE FOR RESIDUE SO4 A 1905 source : AC5 17) chain A residue 1670 type sequence E description BINDING SITE FOR RESIDUE SO4 A 1905 source : AC5 18) chain A residue 1715 type sequence R description BINDING SITE FOR RESIDUE SO4 A 1905 source : AC5 19) chain B residue 46 type sequence A description BINDING SITE FOR RESIDUE SO4 A 1905 source : AC5 20) chain A residue 1652 type sequence H description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 21) chain A residue 1655 type sequence L description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 22) chain A residue 1656 type sequence A description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 23) chain A residue 1686 type sequence K description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 24) chain A residue 1689 type sequence C description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 25) chain B residue 48 type sequence K description BINDING SITE FOR RESIDUE SO4 A 1906 source : AC6 26) chain A residue 1582 type sequence V description BINDING SITE FOR RESIDUE SO4 A 1907 source : AC7 27) chain A residue 1602 type sequence D description BINDING SITE FOR RESIDUE SO4 A 1907 source : AC7 28) chain A residue 1764 type sequence R description BINDING SITE FOR RESIDUE SO4 A 1907 source : AC7 29) chain A residue 1515 type sequence F description BINDING SITE FOR RESIDUE SO4 A 1908 source : AC8 30) chain A residue 1565 type sequence Y description BINDING SITE FOR RESIDUE SO4 A 1908 source : AC8 31) chain A residue 1568 type sequence K description BINDING SITE FOR RESIDUE SO4 A 1908 source : AC8 32) chain A residue 1590 type sequence N description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 33) chain A residue 1592 type sequence C description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 34) chain A residue 1673 type sequence N description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 35) chain A residue 1758 type sequence G description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 36) chain A residue 1759 type sequence H description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 37) chain B residue 75 type sequence G description BINDING SITE FOR RESIDUE 3CN B 101 source : AC9 38) chain A residue 1705 type sequence Y description BINDING SITE FOR RESIDUE SO4 B 102 source : BC1 39) chain A residue 1715 type sequence R description BINDING SITE FOR RESIDUE SO4 B 102 source : BC1 40) chain B residue 66 type sequence T description BINDING SITE FOR RESIDUE SO4 B 102 source : BC1 41) chain B residue 68 type sequence H description BINDING SITE FOR RESIDUE SO4 B 102 source : BC1 42) chain B residue 31 type sequence Q description BINDING SITE FOR RESIDUE SO4 B 103 source : BC2 43) chain B residue 39 type sequence D description BINDING SITE FOR RESIDUE SO4 B 103 source : BC2 44) chain B residue 72 type sequence R description BINDING SITE FOR RESIDUE SO4 B 103 source : BC2 45) chain B residue 74 type sequence R description BINDING SITE FOR RESIDUE SO4 B 103 source : BC2 46) chain B residue 27-52 type prosite sequence KAKIQDKEGIPPDQQRLIFAGKQLED description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD source prosite : PS00299 47) chain B residue 54 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 48) chain B residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 49) chain B 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_FI10 50) chain B residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 51) chain B 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:25474007, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 52) chain B residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 53) chain B 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_FI5 54) chain B 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_FI6 55) chain B 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_FI7 56) chain B 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_FI7 57) chain B 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_FI8 58) chain B 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_FI9

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