eF-site ID 3u30-ABCDEF
PDB Code 3u30
Chain A, B, C, D, E, F

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Title Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin
Classification IMMUNE SYSTEM
Compound linear di-ubiquitin
Source Homo sapiens (Human) (3U30)
Sequence A:  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP
DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQ
IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQR
LIFAGKQLEDGRTLSDYNIQKESTLHLVL
B:  DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKP
GKAPKLLIYSAKFLYSGVPSRFSGSGSGTDFTLTISSLQP
EDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
LSSPVTKSFNR
C:  VQLVESGGGLVQPGGSLRLSCAASGFTFSNTYISWVRQAP
GKGLEWVASITPSSGQTDYADSVKGRFTISADTSKNTAYL
QMNSLRAEDTAVYYCARTWLLRWVMDLWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWN
SGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYI
CNVNHKPSNTKVDKKVEP
D:  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQ
RLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV
KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF
AGKQLEDGRTLSDYNIQKESTLHLV
E:  DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKP
GKAPKLLIYSAKFLYSGVPSRFSGSGSGTDFTLTISSLQP
EDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
LSSPVTKSFNR
F:  VQLVESGGGLVQPGGSLRLSCAASGFTFSNTYISWVRQAP
GKGLEWVASITPSSGQTDYADSVKGRFTISADTSKNTAYL
QMNSLRAEDTAVYYCARTWLLRWVMDLWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWN
SGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYI
CNVNHKPSNTKVDKKVEP
Description


Functional site
1) chain A
residue 48
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
2) chain D
residue 48
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
3) chain A
residue 37
type SITE
sequence P
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
4) chain A
residue 55
type SITE
sequence T
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
5) chain D
residue 37
type SITE
sequence P
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
6) chain D
residue 55
type SITE
sequence T
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
7) chain A
residue 51
type SITE
sequence E
description Essential for function
source Swiss-Prot : SWS_FT_FI2
8) chain D
residue 51
type SITE
sequence E
description Essential for function
source Swiss-Prot : SWS_FT_FI2
9) chain A
residue 46
type CROSSLNK
sequence A
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_FI11
10) chain D
residue 46
type CROSSLNK
sequence A
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_FI11
11) chain A
residue 49
type MOD_RES
sequence Q
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
12) chain D
residue 49
type MOD_RES
sequence Q
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
13) chain A
residue 10
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
source Swiss-Prot : SWS_FT_FI6
14) chain D
residue 10
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
source Swiss-Prot : SWS_FT_FI6
15) chain A
residue 59
type MOD_RES
sequence Y
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5
16) chain D
residue 59
type MOD_RES
sequence Y
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5
17) chain A
residue 31
type CROSSLNK
sequence Q
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_FI10
18) chain D
residue 31
type CROSSLNK
sequence Q
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_FI10
19) chain A
residue 59
type CROSSLNK
sequence Y
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7
20) chain D
residue 59
type CROSSLNK
sequence Y
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7
21) chain A
residue 12
type CROSSLNK
sequence T
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_FI8
22) chain D
residue 12
type CROSSLNK
sequence T
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_FI8
23) chain A
residue 16
type CROSSLNK
sequence E
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
source Swiss-Prot : SWS_FT_FI9
24) chain D
residue 16
type CROSSLNK
sequence E
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
source Swiss-Prot : SWS_FT_FI9
25) chain A
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299
26) chain A
residue 103-128
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299
27) chain C
residue 194-200
type prosite
sequence YICNVNH
description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YICNVNH
source prosite : PS00290
28) chain B
residue 192-198
type prosite
sequence YACEVTH
description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YICNVNH
source prosite : PS00290

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