eF-site ID 4mm3-AB
PDB Code 4mm3
Chain A, B

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Title Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde
Classification SIGNALING PROTEIN/HYDROLASE
Compound Ubiquitin
Source Homo sapiens (Human) (R1A_CVHSA)
Sequence A:  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGX
B:  MEVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGA
DVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESF
LGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLA
LQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTV
GELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTL
TGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQES
SFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAK
ETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIK
Description (1)  Ubiquitin, Papain-like proteinase (E.C.3.4.19.12, 3.4.22.69)


Functional site

1) chain B
residue 190
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 401
source : AC1

2) chain B
residue 193
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 401
source : AC1

3) chain B
residue 225
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 401
source : AC1

4) chain B
residue 227
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 401
source : AC1

5) 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

6) chain B
residue 190
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00444
source Swiss-Prot : SWS_FT_FI3

7) chain B
residue 193
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00444
source Swiss-Prot : SWS_FT_FI3

8) chain B
residue 225
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00444
source Swiss-Prot : SWS_FT_FI3

9) chain B
residue 227
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00444
source Swiss-Prot : SWS_FT_FI3

10) chain A
residue 66
type MOD_RES
sequence T
description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
source Swiss-Prot : SWS_FT_FI4

11) chain A
residue 76
type MOD_RES
sequence X
description ADP-ribosylglycine => ECO:0000269|PubMed:28525742
source Swiss-Prot : SWS_FT_FI5

12) 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

13) chain B
residue 190-227
type ZN_FING
sequence CKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVC
description C4-type => ECO:0000255|PROSITE-ProRule:PRU00444, ECO:0000269|PubMed:16306590
source Swiss-Prot : SWS_FT_FI1

14) chain A
residue 72
type ZN_FING
sequence R
description C4-type => ECO:0000255|PROSITE-ProRule:PRU00444, ECO:0000269|PubMed:16306590
source Swiss-Prot : SWS_FT_FI1

15) 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

16) 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

17) chain B
residue 112
type ACT_SITE
sequence C
description For PL-PRO activity => ECO:0000255|PROSITE-ProRule:PRU00444, ECO:0000269|PubMed:16306590
source Swiss-Prot : SWS_FT_FI2

18) chain B
residue 273
type ACT_SITE
sequence H
description For PL-PRO activity => ECO:0000255|PROSITE-ProRule:PRU00444, ECO:0000269|PubMed:16306590
source Swiss-Prot : SWS_FT_FI2

19) chain B
residue 287
type ACT_SITE
sequence D
description For PL-PRO activity => ECO:0000255|PROSITE-ProRule:PRU00444, ECO:0000269|PubMed:16306590
source Swiss-Prot : SWS_FT_FI2

20) chain A
residue 76
type CROSSLNK
sequence X
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI7

21) 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

22) 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

23) 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

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


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