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2KWO

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at Serine 1

Functional Information from GO Data
ChainGOidnamespacecontents
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ZN A 501
ChainResidue
ACYS262
ACYS265
AASN272
AHIS292
ACYS295

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 601
ChainResidue
ACYS284
ACYS287
ACYS313
ACYS316

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ZN A 701
ChainResidue
ACYS334
ACYS337
AARG339
ACYS360
ACYS363

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 801
ChainResidue
ACYS319
ACYS322
AHIS342
ACYS345

Functional Information from PROSITE/UniProt
site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18

site_idPS01359
Number of Residues80
DetailsZF_PHD_1 Zinc finger PHD-type signature. CadCgrsghptclqftlnmteavktykwqcieckscilcgtsenddql.LfCdd..Cdrg.YHmyClnppvaeppegs.................................WsChlC
ChainResidueDetails
ACYS284-CYS363

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsModified residue: {"description":"Symmetric dimethylarginine; by PRMT5 and PRMT7; alternate","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"N6-lactoyllysine; alternate","evidences":[{"source":"PubMed","id":"31645732","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"17267393","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues50
DetailsZinc finger: {"description":"PHD-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00146","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues15
DetailsRegion: {"description":"Interaction with HDGFL2","evidences":[{"source":"PubMed","id":"32459350","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"32459350","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

239492

PDB entries from 2025-07-30

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