eF-site ID 4rf0-AB
PDB Code 4rf0
Chain A, B

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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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