eF-site ID 3dvn-ABHLUVXY
PDB Code 3dvn
Chain A, B, H, L, U, V, X, Y

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Title Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin
Classification IMMUNE SYSTEM
Compound Human IgG1 fab fragment light chain
Source (UBIQ_HUMAN)
Sequence A:  TQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAP
KLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFA
TYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES
VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS
SPVTKSFNRGEC
B:  EVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQA
PGKGLEWVAYISPYYGSTSYADSVKGRFTISADTSKNTAY
LQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSS
ASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPK
H:  EVQLVESGGGLVQPGGSLRLSCAASGFNVKTGLIHWVRQA
PGKGLEWVAYISPYYGSTSYADSVKGRFTISADTSKNTAY
LQMNSLRAEDTAVYYCAREYYRWYTAIDYWGQGTLVTVSS
ASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPK
L:  TQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAP
KLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFA
TYYCQQYSSYSSLFTFGQGTKVEIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES
VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS
SPVTKSFNRGEC
U:  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP
DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL
V:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
X:  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP
DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL
Y:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
Description


Functional site
1) chain Y
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
2) chain Y
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
3) chain V
residue 54
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
4) chain V
residue 72
type SITE
sequence R
description Interacts with activating enzyme
source Swiss-Prot : SWS_FT_FI1
5) chain Y
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2
6) chain V
residue 68
type SITE
sequence H
description Essential for function
source Swiss-Prot : SWS_FT_FI2
7) chain Y
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
8) chain V
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
9) chain Y
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
10) chain V
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
11) chain Y
residue 63
type CROSSLNK
sequence R
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
12) chain V
residue 63
type CROSSLNK
sequence R
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
13) chain Y
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
14) chain Y
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
15) chain V
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
16) chain V
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
17) chain Y
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
18) chain V
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4
19) chain Y
residue 76
type MOD_RES
sequence G
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5
20) chain V
residue 76
type MOD_RES
sequence G
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5
21) chain Y
residue 76
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7
22) chain V
residue 76
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7
23) chain Y
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
24) chain V
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
25) chain Y
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
26) chain V
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
27) chain Y
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
28) chain V
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
29) chain X
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299
30) chain Y
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299
31) chain A
residue 194-200
type prosite
sequence YACEVTH
description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACEVTH
source prosite : PS00290
32) chain B
residue 201-207
type prosite
sequence YICNVNH
description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACEVTH
source prosite : PS00290

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