eF-site ID 3phd-ABCDEFGH PDB Code 3phd Chain A, B, C, D, E, F, G, H click to enlarge Title Crystal structure of human HDAC6 in complex with ubiquitin Classification PROTEIN BINDING Compound Histone deacetylase 6 Source Homo sapiens (Human) (UBB_HUMAN) Sequence A:  PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSC YQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQA YVHHQALLDVKNIAHQNKFGED B:  PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSC YQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQA YVHHQALLDVKNIAHQNKFG C:  PWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQ VYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYV HHQAL D:  WCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQV YCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH HQAL E:  IENVKLHLLRLRGG F:  RLRGG G:  VKTLTGKTITVEPTIENVKAKIQQLIFESTLHLVLRLRGG H:  VKTLTGKTPSTIENVKAKIQQRLIFAGIQKELVLRLRGG Description Functional site 1) chain A residue 37 type sequence C description BINDING SITE FOR RESIDUE ZN A 1000 source : AC1 2) chain A residue 40 type sequence C description BINDING SITE FOR RESIDUE ZN A 1000 source : AC1 3) chain A residue 56 type sequence H description BINDING SITE FOR RESIDUE ZN A 1000 source : AC1 4) chain A residue 62 type sequence H description BINDING SITE FOR RESIDUE ZN A 1000 source : AC1 5) chain A residue 25 type sequence C description BINDING SITE FOR RESIDUE ZN A 1001 source : AC2 6) chain A residue 28 type sequence C description BINDING SITE FOR RESIDUE ZN A 1001 source : AC2 7) chain A residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN A 1001 source : AC2 8) chain A residue 52 type sequence H description BINDING SITE FOR RESIDUE ZN A 1001 source : AC2 9) chain A residue 5 type sequence C description BINDING SITE FOR RESIDUE ZN A 1002 source : AC3 10) chain A residue 7 type sequence H description BINDING SITE FOR RESIDUE ZN A 1002 source : AC3 11) chain A residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN A 1002 source : AC3 12) chain A residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN A 1002 source : AC3 13) chain B residue 37 type sequence C description BINDING SITE FOR RESIDUE ZN B 2000 source : AC4 14) chain B residue 40 type sequence C description BINDING SITE FOR RESIDUE ZN B 2000 source : AC4 15) chain B residue 56 type sequence H description BINDING SITE FOR RESIDUE ZN B 2000 source : AC4 16) chain B residue 62 type sequence H description BINDING SITE FOR RESIDUE ZN B 2000 source : AC4 17) chain B residue 25 type sequence C description BINDING SITE FOR RESIDUE ZN B 2001 source : AC5 18) chain B residue 28 type sequence C description BINDING SITE FOR RESIDUE ZN B 2001 source : AC5 19) chain B residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN B 2001 source : AC5 20) chain B residue 52 type sequence H description BINDING SITE FOR RESIDUE ZN B 2001 source : AC5 21) chain B residue 5 type sequence C description BINDING SITE FOR RESIDUE ZN B 2002 source : AC6 22) chain B residue 7 type sequence H description BINDING SITE FOR RESIDUE ZN B 2002 source : AC6 23) chain B residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN B 2002 source : AC6 24) chain B residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN B 2002 source : AC6 25) chain C residue 37 type sequence C description BINDING SITE FOR RESIDUE ZN C 2000 source : AC7 26) chain C residue 40 type sequence C description BINDING SITE FOR RESIDUE ZN C 2000 source : AC7 27) chain C residue 56 type sequence H description BINDING SITE FOR RESIDUE ZN C 2000 source : AC7 28) chain C residue 62 type sequence H description BINDING SITE FOR RESIDUE ZN C 2000 source : AC7 29) chain C residue 25 type sequence C description BINDING SITE FOR RESIDUE ZN C 2001 source : AC8 30) chain C residue 28 type sequence C description BINDING SITE FOR RESIDUE ZN C 2001 source : AC8 31) chain C residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN C 2001 source : AC8 32) chain C residue 52 type sequence H description BINDING SITE FOR RESIDUE ZN C 2001 source : AC8 33) chain C residue 5 type sequence C description BINDING SITE FOR RESIDUE ZN C 2002 source : AC9 34) chain C residue 7 type sequence H description BINDING SITE FOR RESIDUE ZN C 2002 source : AC9 35) chain C residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN C 2002 source : AC9 36) chain C residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN C 2002 source : AC9 37) chain D residue 37 type sequence C description BINDING SITE FOR RESIDUE ZN D 2000 source : BC1 38) chain D residue 40 type sequence C description BINDING SITE FOR RESIDUE ZN D 2000 source : BC1 39) chain D residue 56 type sequence H description BINDING SITE FOR RESIDUE ZN D 2000 source : BC1 40) chain D residue 62 type sequence H description BINDING SITE FOR RESIDUE ZN D 2000 source : BC1 41) chain D residue 25 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : BC2 42) chain D residue 28 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : BC2 43) chain D residue 45 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : BC2 44) chain D residue 52 type sequence H description BINDING SITE FOR RESIDUE ZN D 2001 source : BC2 45) chain D residue 5 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : BC3 46) chain D residue 7 type sequence H description BINDING SITE FOR RESIDUE ZN D 2002 source : BC3 47) chain D residue 75 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : BC3 48) chain D residue 78 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : BC3 49) chain E residue 76 type MOD_RES sequence G description ADP-ribosylglycine => ECO:0000269|PubMed:28525742 source Swiss-Prot : SWS_FT_FI5 50) chain F residue 76 type MOD_RES sequence G description ADP-ribosylglycine => ECO:0000269|PubMed:28525742 source Swiss-Prot : SWS_FT_FI5 51) chain G residue 76 type MOD_RES sequence G description ADP-ribosylglycine => ECO:0000269|PubMed:28525742 source Swiss-Prot : SWS_FT_FI5 52) chain H residue 76 type MOD_RES sequence G description ADP-ribosylglycine => ECO:0000269|PubMed:28525742 source Swiss-Prot : SWS_FT_FI5 53) chain H residue 63 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 source Swiss-Prot : SWS_FT_FI12 54) chain G residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 55) chain H residue 6 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 source Swiss-Prot : SWS_FT_FI6 56) chain G residue 66 type MOD_RES sequence T description (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 source Swiss-Prot : SWS_FT_FI4 57) chain E residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 58) chain F residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 59) chain G residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 60) chain H residue 72 type SITE sequence R description Interacts with activating enzyme source Swiss-Prot : SWS_FT_FI1 61) chain E residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 62) chain A residue 62 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 63) chain A residue 75 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 64) chain A residue 78 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 65) chain B residue 5 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 66) chain B residue 7 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 67) chain B residue 25 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 68) chain B residue 28 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 69) chain B residue 37 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 70) chain B residue 40 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 71) chain B residue 45 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 72) chain B residue 52 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 73) chain B residue 56 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 74) chain B residue 62 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 75) chain B residue 75 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 76) chain B residue 78 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 77) chain C residue 5 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 78) chain C residue 7 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 79) chain C residue 25 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 80) chain C residue 28 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 81) chain C residue 37 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 82) chain G residue 68 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 83) chain C residue 40 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 84) chain C residue 45 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 85) chain C residue 52 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 86) chain C residue 56 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 87) chain C residue 62 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 88) chain C residue 75 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 89) chain C residue 78 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 90) chain D residue 5 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 91) chain D residue 7 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 92) chain D residue 25 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 93) chain D residue 28 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 94) chain D residue 37 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 95) chain D residue 40 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 96) chain D residue 45 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 97) chain D residue 52 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 98) chain D residue 56 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 99) chain D residue 62 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 100) chain D residue 75 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 101) chain D residue 78 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 102) chain A residue 37 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 103) chain A residue 40 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 104) chain A residue 45 type SITE sequence C description Essential for function source Swiss-Prot : SWS_FT_FI2 105) chain A residue 52 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 106) chain A residue 56 type SITE sequence H description Essential for function source Swiss-Prot : SWS_FT_FI2 107) chain G residue 65 type MOD_RES sequence S description Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 source Swiss-Prot : SWS_FT_FI3 108) chain G residue 29 type CROSSLNK sequence K description 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 source Swiss-Prot : SWS_FT_FI10 109) chain H residue 29 type CROSSLNK sequence K description 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 source Swiss-Prot : SWS_FT_FI10 110) chain E residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 111) chain G residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 112) chain H residue 27 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 source Swiss-Prot : SWS_FT_FI9 113) chain E residue 76 type CROSSLNK sequence G description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) source Swiss-Prot : SWS_FT_FI7 114) chain F residue 76 type CROSSLNK sequence G description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) source Swiss-Prot : SWS_FT_FI7 115) chain G residue 76 type CROSSLNK sequence G description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) source Swiss-Prot : SWS_FT_FI7 116) chain H residue 76 type CROSSLNK sequence G description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) source Swiss-Prot : SWS_FT_FI7 117) chain G residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8 118) chain H residue 11 type CROSSLNK sequence K description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 source Swiss-Prot : SWS_FT_FI8

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