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4M0W

Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin

Functional Information from GO Data
ChainGOidnamespacecontents
A0006508biological_processproteolysis
A0008234molecular_functioncysteine-type peptidase activity
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 401
ChainResidue
ACYS190
ACYS193
ACYS225
ACYS227

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 402
ChainResidue
ASER112
ASER115
ASER116
ATYR274
AHOH702

site_idAC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE NHE A 403
ChainResidue
ALYS106
ATRP107
AASP287
AGLY288
AALA289
AHIS290
ATHR313
AILE315
AHOH520
AHOH561
AHOH742

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NHE A 404
ChainResidue
AGLN123
ALEU124
AGLU125
AARG141
AHOH703

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 405
ChainResidue
AHIS18
AGLN20
AASP62
ATHR64
ALEU65
AHOH639

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 406
ChainResidue
ATYR252
ALYS253
ALEU254
AGLN255
ATHR258
ATYR306

site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL B 101
ChainResidue
BGLU24
BASN25
BALA28

Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues55
DetailsDomain: {"description":"Ubiquitin-like 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues37
DetailsZinc finger: {"description":"C4-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00444","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16306590","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues1
DetailsActive site: {"description":"For PL-PRO activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU00444","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsActive site: {"description":"For PL-PRO activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU00444","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16306590","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00444","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues75
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues1
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues1
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues7
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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