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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 Residues8
DetailsSITE: Interacts with activating enzyme
ChainResidueDetails
EARG54
EARG72
FARG54
FARG72
GARG54
GARG72
HARG54
HARG72

site_idSWS_FT_FI2
Number of Residues4
DetailsSITE: Essential for function
ChainResidueDetails
EHIS68
AHIS62
ACYS75
ACYS78
BCYS5
BHIS7
BCYS25
BCYS28
BCYS37
BCYS40
BCYS45
FHIS68
BHIS52
BHIS56
BHIS62
BCYS75
BCYS78
CCYS5
CHIS7
CCYS25
CCYS28
CCYS37
GHIS68
CCYS40
CCYS45
CHIS52
CHIS56
CHIS62
CCYS75
CCYS78
DCYS5
DHIS7
DCYS25
HHIS68
DCYS28
DCYS37
DCYS40
DCYS45
DHIS52
DHIS56
DHIS62
DCYS75
DCYS78
ACYS37
ACYS40
ACYS45
AHIS52
AHIS56

site_idSWS_FT_FI3
Number of Residues4
DetailsMOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
ChainResidueDetails
ESER65
FSER65
GSER65
HSER65

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
ChainResidueDetails
ETHR66
FTHR66
GTHR66
HTHR66

site_idSWS_FT_FI5
Number of Residues4
DetailsMOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742
ChainResidueDetails
EGLY76
FGLY76
GGLY76
HGLY76

site_idSWS_FT_FI6
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603
ChainResidueDetails
ELYS6
FLYS6
GLYS6
HLYS6

site_idSWS_FT_FI7
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
ChainResidueDetails
EGLY76
FGLY76
GGLY76
HGLY76

site_idSWS_FT_FI8
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
ChainResidueDetails
ELYS11
ELYS48
FLYS11
FLYS48
GLYS11
GLYS48
HLYS11
HLYS48

site_idSWS_FT_FI9
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
ChainResidueDetails
ELYS27
FLYS27
GLYS27
HLYS27

site_idSWS_FT_FI10
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127
ChainResidueDetails
ELYS29
FLYS29
GLYS29
HLYS29

site_idSWS_FT_FI11
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
ChainResidueDetails
ELYS33
FLYS33
GLYS33
HLYS33

site_idSWS_FT_FI12
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106
ChainResidueDetails
ELYS63
FLYS63
GLYS63
HLYS63

225158

PDB entries from 2024-09-18

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