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


Display surface

Download
Links