eF-site ID 2wdt-ABCD
PDB Code 2wdt
Chain A, B, C, D

click to enlarge
Title Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME
Classification HYDROLASE/PROTEIN BINDING
Compound UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
Source (2WDT)
Sequence A:  DIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDM
IPQPVQAVIFLYPVNFDNVWFIKQYIPNSCGTIALLHLYG
NLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIE
NLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRK
DHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALA
VIPN
B:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGX
C:  NDIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLD
MIPQPVQAVIFLYPVNFDNVWFIKQYIPNSCGTIALLHLY
GNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSI
ENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGR
KDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSAL
AVIPND
D:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGX
Description


Functional site

1) chain D
residue 42
type
sequence R
description BINDING SITE FOR RESIDUE CL D 1076
source : AC1

2) chain B
residue 42
type
sequence R
description BINDING SITE FOR RESIDUE CL B 1076
source : AC2

3) chain B
residue 27-52
type prosite
sequence KAKIQDKEGIPPDQQRLIFAGKQLED
description UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
source prosite : PS00299

4) chain A
residue 92
type ACT_SITE
sequence C
description Nucleophile => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI1

5) chain C
residue 92
type ACT_SITE
sequence C
description Nucleophile => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI1

6) chain D
residue 54
type ACT_SITE
sequence R
description Nucleophile => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI1

7) chain D
residue 72
type ACT_SITE
sequence R
description Nucleophile => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI1

8) 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

9) chain D
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

10) chain A
residue 164
type ACT_SITE
sequence H
description Proton donor => ECO:0000250|UniProtKB:P09936
source Swiss-Prot : SWS_FT_FI2

11) chain C
residue 164
type ACT_SITE
sequence H
description Proton donor => ECO:0000250|UniProtKB:P09936
source Swiss-Prot : SWS_FT_FI2

12) chain A
residue 33
type SITE
sequence D
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

13) chain A
residue 157
type SITE
sequence D
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

14) chain A
residue 219
type SITE
sequence S
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

15) chain C
residue 33
type SITE
sequence D
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

16) chain C
residue 157
type SITE
sequence D
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

17) chain C
residue 219
type SITE
sequence S
description Interaction with ubiquitin => ECO:0000269|PubMed:20042598
source Swiss-Prot : SWS_FT_FI3

18) chain A
residue 179
type SITE
sequence D
description Important for enzyme activity => ECO:0000250|UniProtKB:P09936
source Swiss-Prot : SWS_FT_FI4

19) chain C
residue 179
type SITE
sequence D
description Important for enzyme activity => ECO:0000250|UniProtKB:P09936
source Swiss-Prot : SWS_FT_FI4

20) 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

21) chain D
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

22) 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

23) chain D
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

24) 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

25) 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

26) chain D
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

27) chain D
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

28) 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

29) chain D
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

30) 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

31) chain D
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


Display surface

Download
Links