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4XKL

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin

Functional Information from PDB Data
site_idAC1
Number of Residues9
Detailsbinding site for residue GOL A 101
ChainResidue
ATHR7
ALEU8
ATHR9
ALEU69
AVAL70
ALEU71
AHOH213
CLEU71
DHOH601

site_idAC2
Number of Residues4
Detailsbinding site for residue ACT B 502
ChainResidue
BASP426
BLYS427
BILE428
BHOH615

site_idAC3
Number of Residues4
Detailsbinding site for residue ZN B 503
ChainResidue
BCYS422
BCYS425
BHIS440
BHIS444

site_idAC4
Number of Residues8
Detailsbinding site for residue GOL C 101
ChainResidue
CTHR7
CLEU8
CTHR9
CLEU69
CVAL70
CLEU71
CHOH207
CHOH208

site_idAC5
Number of Residues2
Detailsbinding site for residue ACT C 102
ChainResidue
CLYS11
CTHR12

site_idAC6
Number of Residues1
Detailsbinding site for residue ACT D 501
ChainResidue
DCYS419

site_idAC7
Number of Residues4
Detailsbinding site for residue ZN D 502
ChainResidue
DCYS422
DCYS425
DHIS440
DHIS444

Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
ALYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues150
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues4
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25474007","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues50
DetailsZinc finger: {"description":"UBZ1-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01253","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01253","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

243531

PDB entries from 2025-10-22

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