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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3PHD

Crystal structure of human HDAC6 in complex with ubiquitin

Functional Information from GO Data
ChainGOidnamespacecontents
A0008270molecular_functionzinc ion binding
B0008270molecular_functionzinc ion binding
C0008270molecular_functionzinc ion binding
D0008270molecular_functionzinc ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1000
ChainResidue
ACYS37
ACYS40
AHIS56
AHIS62
site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1001
ChainResidue
ACYS25
ACYS28
ACYS45
AHIS52
site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1002
ChainResidue
AHIS7
ACYS75
ACYS78
ACYS5
site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 2000
ChainResidue
BCYS37
BCYS40
BHIS56
BHIS62
site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 2001
ChainResidue
BCYS25
BCYS28
BCYS45
BHIS52
site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 2002
ChainResidue
BCYS5
BHIS7
BCYS75
BCYS78
site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN C 2000
ChainResidue
CCYS37
CCYS40
CHIS56
CHIS62
site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN C 2001
ChainResidue
CCYS25
CCYS28
CCYS45
CHIS52
site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN C 2002
ChainResidue
CCYS5
CHIS7
CCYS75
CCYS78
site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 2000
ChainResidue
DCYS37
DCYS40
DHIS56
DHIS62
site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 2001
ChainResidue
DCYS25
DCYS28
DCYS45
DHIS52
site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 2002
ChainResidue
DCYS5
DHIS7
DCYS75
DCYS78
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
ELYS27-ASP52
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues98
DetailsZinc finger: {"description":"UBP-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00502","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues36
DetailsRegion: {"description":"Ubiquitin binding","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues48
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00502","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2008","submissionDatabase":"PDB data bank","title":"Crystal structure of human HDAC6 zinc finger domain.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues3
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_FI8
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues1
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":"25527291","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
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":"16443603","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":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","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":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
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

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PDB entries from 2025-11-05

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