eF-site ID 4k7w-ABC
PDB Code 4k7w
Chain A, B, C

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Title Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb
Classification LIGASE
Compound ubiquitin
Source Homo sapiens (Human) (UBC_HUMAN)
Sequence A:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
B:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
C:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
Description


Functional site
1) chain A
residue 1
type
sequence M
description BINDING SITE FOR RESIDUE ZN A 101
source : AC1
2) chain A
residue 16
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 101
source : AC1
3) chain B
residue 51
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 101
source : AC1
4) chain A
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 102
source : AC2
5) chain C
residue 21
type
sequence D
description BINDING SITE FOR RESIDUE ZN A 102
source : AC2
6) chain A
residue 21
type
sequence D
description BINDING SITE FOR RESIDUE ZN A 103
source : AC3
7) chain B
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 103
source : AC3
8) chain A
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 104
source : AC4
9) chain B
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 104
source : AC4
10) chain C
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN A 104
source : AC4
11) chain A
residue 6
type
sequence K
description BINDING SITE FOR RESIDUE ACT A 105
source : AC5
12) chain A
residue 66
type
sequence T
description BINDING SITE FOR RESIDUE ACT A 105
source : AC5
13) chain A
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ACT A 105
source : AC5
14) chain B
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ACT A 105
source : AC5
15) chain A
residue 16
type
sequence E
description BINDING SITE FOR RESIDUE EDO A 106
source : AC6
16) chain A
residue 17
type
sequence V
description BINDING SITE FOR RESIDUE EDO A 106
source : AC6
17) chain A
residue 21
type
sequence D
description BINDING SITE FOR RESIDUE EDO A 106
source : AC6
18) chain A
residue 29
type
sequence K
description BINDING SITE FOR RESIDUE EDO A 106
source : AC6
19) chain B
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE EDO A 106
source : AC6
20) chain A
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ZN B 101
source : AC7
21) chain B
residue 6
type
sequence K
description BINDING SITE FOR RESIDUE ZN B 101
source : AC7
22) chain B
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ZN B 101
source : AC7
23) chain B
residue 1
type
sequence M
description BINDING SITE FOR RESIDUE ZN B 102
source : AC8
24) chain B
residue 16
type
sequence E
description BINDING SITE FOR RESIDUE ZN B 102
source : AC8
25) chain C
residue 51
type
sequence E
description BINDING SITE FOR RESIDUE ZN B 102
source : AC8
26) chain A
residue 51
type
sequence E
description BINDING SITE FOR RESIDUE ZN C 101
source : AC9
27) chain C
residue 1
type
sequence M
description BINDING SITE FOR RESIDUE ZN C 101
source : AC9
28) chain C
residue 16
type
sequence E
description BINDING SITE FOR RESIDUE ZN C 101
source : AC9
29) chain B
residue 21
type
sequence D
description BINDING SITE FOR RESIDUE ZN C 102
source : BC1
30) chain C
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ZN C 102
source : BC1
31) chain A
residue 39
type
sequence D
description BINDING SITE FOR RESIDUE ZN C 103
source : BC2
32) chain C
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ZN C 103
source : BC2
33) chain A
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ACT C 104
source : BC3
34) chain C
residue 16
type
sequence E
description BINDING SITE FOR RESIDUE ACT C 104
source : BC3
35) chain C
residue 18
type
sequence E
description BINDING SITE FOR RESIDUE ACT C 104
source : BC3
36) chain C
residue 21
type
sequence D
description BINDING SITE FOR RESIDUE ACT C 104
source : BC3
37) chain C
residue 29
type
sequence K
description BINDING SITE FOR RESIDUE ACT C 104
source : BC3
38) chain A
residue 39
type
sequence D
description BINDING SITE FOR RESIDUE ACT C 105
source : BC4
39) chain C
residue 6
type
sequence K
description BINDING SITE FOR RESIDUE ACT C 105
source : BC4
40) chain C
residue 68
type
sequence H
description BINDING SITE FOR RESIDUE ACT C 105
source : BC4
41) chain A
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299
42) chain A
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
43) chain A
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
44) chain B
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
45) chain B
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
46) chain C
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
47) chain C
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
48) 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
49) 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_FI10
50) chain C
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
51) 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
52) 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_FI11
53) chain C
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
54) 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
55) 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_FI12
56) chain C
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
57) chain A
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2
58) chain B
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2
59) chain C
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2
60) 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
61) 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:25527291
source Swiss-Prot : SWS_FT_FI3
62) chain C
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
63) chain A
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
64) chain B
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
65) chain C
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
66) 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
67) 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_FI6
68) chain C
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
69) 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
70) 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
71) 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_FI8
72) 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_FI8
73) chain C
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
74) chain C
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
75) 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
76) 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_FI9
77) chain C
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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