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4UDM

Crystal structure of Im3 in complex with Y52A mutant of E3RNase

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0015643molecular_functiontoxic substance binding
A0030153biological_processbacteriocin immunity
B0003723molecular_functionRNA binding
B0016788molecular_functionhydrolase activity, acting on ester bonds
B0043022molecular_functionribosome binding
Functional Information from PDB Data
site_idAC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE CA A 1086
ChainResidue
ASER70
AASP71

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE CA B 1097
ChainResidue
BASP55
BHIS58
BGLU60
BGLU62

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 1098
ChainResidue
BARG40
BARG42
BGLU53
BPRO29
BLYS30
BTHR31

site_idAC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL A 1087
ChainResidue
ALYS24

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues94
DetailsRegion: {"description":"Cytotoxic RNase (C) domain","evidences":[{"source":"PubMed","id":"11741540","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues34
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues21
DetailsRegion: {"description":"Binding of immunity protein"}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"11741540","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"20852642","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues1
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"11741540","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"20852642","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues1
DetailsActive site: {"evidences":[{"source":"PubMed","id":"11741540","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues1
DetailsSite: {"description":"Stabilizes positive charge on His-513","evidences":[{"source":"PubMed","id":"20852642","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues4
DetailsM-CSA 530
ChainResidueDetails
BASP55electrostatic stabiliser, increase acidity
BHIS58promote heterolysis, proton acceptor, proton donor
BGLU62increase nucleophilicity, promote heterolysis, proton acceptor, proton donor
BARG90electrostatic stabiliser

246704

PDB entries from 2025-12-24

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