5THT
Crystal Structure of G303A HDAC8 in complex with M344
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000118 | cellular_component | histone deacetylase complex |
| A | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| A | 0000228 | cellular_component | nuclear chromosome |
| A | 0004407 | molecular_function | histone deacetylase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006325 | biological_process | chromatin organization |
| A | 0007064 | biological_process | mitotic sister chromatid cohesion |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0030544 | molecular_function | Hsp70 protein binding |
| A | 0031397 | biological_process | negative regulation of protein ubiquitination |
| A | 0031507 | biological_process | heterochromatin formation |
| A | 0031647 | biological_process | regulation of protein stability |
| A | 0032204 | biological_process | regulation of telomere maintenance |
| A | 0033558 | molecular_function | protein lysine deacetylase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051879 | molecular_function | Hsp90 protein binding |
| A | 0140297 | molecular_function | DNA-binding transcription factor binding |
| A | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| A | 0160008 | molecular_function | protein decrotonylase activity |
| A | 0160009 | molecular_function | histone decrotonylase activity |
| B | 0000118 | cellular_component | histone deacetylase complex |
| B | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| B | 0000228 | cellular_component | nuclear chromosome |
| B | 0004407 | molecular_function | histone deacetylase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006325 | biological_process | chromatin organization |
| B | 0007064 | biological_process | mitotic sister chromatid cohesion |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0030544 | molecular_function | Hsp70 protein binding |
| B | 0031397 | biological_process | negative regulation of protein ubiquitination |
| B | 0031507 | biological_process | heterochromatin formation |
| B | 0031647 | biological_process | regulation of protein stability |
| B | 0032204 | biological_process | regulation of telomere maintenance |
| B | 0033558 | molecular_function | protein lysine deacetylase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051879 | molecular_function | Hsp90 protein binding |
| B | 0140297 | molecular_function | DNA-binding transcription factor binding |
| B | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| B | 0160008 | molecular_function | protein decrotonylase activity |
| B | 0160009 | molecular_function | histone decrotonylase activity |
| C | 0000118 | cellular_component | histone deacetylase complex |
| C | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| C | 0000228 | cellular_component | nuclear chromosome |
| C | 0004407 | molecular_function | histone deacetylase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005694 | cellular_component | chromosome |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006325 | biological_process | chromatin organization |
| C | 0007064 | biological_process | mitotic sister chromatid cohesion |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0030544 | molecular_function | Hsp70 protein binding |
| C | 0031397 | biological_process | negative regulation of protein ubiquitination |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0031647 | biological_process | regulation of protein stability |
| C | 0032204 | biological_process | regulation of telomere maintenance |
| C | 0033558 | molecular_function | protein lysine deacetylase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0051879 | molecular_function | Hsp90 protein binding |
| C | 0140297 | molecular_function | DNA-binding transcription factor binding |
| C | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| C | 0160008 | molecular_function | protein decrotonylase activity |
| C | 0160009 | molecular_function | histone decrotonylase activity |
| D | 0000118 | cellular_component | histone deacetylase complex |
| D | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| D | 0000228 | cellular_component | nuclear chromosome |
| D | 0004407 | molecular_function | histone deacetylase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006325 | biological_process | chromatin organization |
| D | 0007064 | biological_process | mitotic sister chromatid cohesion |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0030544 | molecular_function | Hsp70 protein binding |
| D | 0031397 | biological_process | negative regulation of protein ubiquitination |
| D | 0031507 | biological_process | heterochromatin formation |
| D | 0031647 | biological_process | regulation of protein stability |
| D | 0032204 | biological_process | regulation of telomere maintenance |
| D | 0033558 | molecular_function | protein lysine deacetylase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0051879 | molecular_function | Hsp90 protein binding |
| D | 0140297 | molecular_function | DNA-binding transcription factor binding |
| D | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| D | 0160008 | molecular_function | protein decrotonylase activity |
| D | 0160009 | molecular_function | histone decrotonylase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue B3N A 401 |
| Chain | Residue |
| A | HIS142 |
| A | HOH536 |
| B | PRO273 |
| A | HIS143 |
| A | GLY151 |
| A | ASP178 |
| A | HIS180 |
| A | PHE208 |
| A | ASP267 |
| A | TYR306 |
| A | ZN402 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 402 |
| Chain | Residue |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| A | B3N401 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue K A 403 |
| Chain | Residue |
| A | ASP176 |
| A | ASP178 |
| A | HIS180 |
| A | SER199 |
| A | LEU200 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue K A 404 |
| Chain | Residue |
| A | PHE189 |
| A | THR192 |
| A | VAL195 |
| A | TYR225 |
| A | HOH505 |
| A | HOH543 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | PRO281 |
| A | VAL282 |
| A | TYR317 |
| A | LEU346 |
| A | GLU347 |
| A | ILE348 |
| A | HOH507 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | GLN363 |
| A | HOH501 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | TYR111 |
| A | TRP141 |
| A | PHE152 |
| A | CYS153 |
| A | TYR154 |
| A | LEU155 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | ASN307 |
| A | LEU308 |
| A | ALA309 |
| A | ALA339 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | SER63 |
| A | MET64 |
| A | GLU65 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | VAL133 |
| A | LEU292 |
| A | GLN295 |
| A | LEU296 |
| site_id | AD2 |
| Number of Residues | 16 |
| Details | binding site for residue B3N B 401 |
| Chain | Residue |
| A | LYS33 |
| A | PHE152 |
| A | PRO273 |
| B | ASP101 |
| B | HIS142 |
| B | HIS143 |
| B | GLY151 |
| B | PHE152 |
| B | ASP178 |
| B | HIS180 |
| B | PHE208 |
| B | ASP267 |
| B | TYR306 |
| B | ZN402 |
| B | HOH553 |
| B | HOH556 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 402 |
| Chain | Residue |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | B3N401 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue K B 403 |
| Chain | Residue |
| B | ASP176 |
| B | ASP178 |
| B | HIS180 |
| B | SER199 |
| B | LEU200 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue K B 404 |
| Chain | Residue |
| B | PHE189 |
| B | THR192 |
| B | VAL195 |
| B | TYR225 |
| B | HOH506 |
| B | HOH537 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | PRO281 |
| B | VAL282 |
| B | TYR317 |
| B | LEU346 |
| B | GLU347 |
| B | HOH508 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | GLN363 |
| B | HOH501 |
| D | TYR24 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | TYR111 |
| B | TRP141 |
| B | PHE152 |
| B | CYS153 |
| B | TYR154 |
| B | LEU155 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | GLN364 |
| B | ASN367 |
| D | VAL61 |
| D | ASP110 |
| B | GLN363 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| B | ALA62 |
| D | TYR368 |
| site_id | AE2 |
| Number of Residues | 12 |
| Details | binding site for residue B3N C 401 |
| Chain | Residue |
| C | ASP101 |
| C | HIS142 |
| C | HIS143 |
| C | GLY151 |
| C | PHE152 |
| C | ASP178 |
| C | HIS180 |
| C | PHE208 |
| C | ASP267 |
| C | TYR306 |
| C | ZN402 |
| C | HOH511 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 402 |
| Chain | Residue |
| C | ASP178 |
| C | HIS180 |
| C | ASP267 |
| C | B3N401 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue K C 403 |
| Chain | Residue |
| C | ASP176 |
| C | ASP178 |
| C | HIS180 |
| C | SER199 |
| C | LEU200 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue K C 404 |
| Chain | Residue |
| C | PHE189 |
| C | THR192 |
| C | VAL195 |
| C | TYR225 |
| C | HOH502 |
| C | HOH528 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 405 |
| Chain | Residue |
| C | LYS132 |
| C | LEU292 |
| C | GLN295 |
| C | LEU296 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 406 |
| Chain | Residue |
| C | PRO281 |
| C | LEU346 |
| C | GLU347 |
| C | ILE348 |
| C | EDO410 |
| site_id | AE8 |
| Number of Residues | 10 |
| Details | binding site for residue EDO C 407 |
| Chain | Residue |
| C | LEU179 |
| C | ASP267 |
| C | THR268 |
| C | ILE269 |
| C | ALA270 |
| C | ASP272 |
| C | CYS275 |
| C | SER276 |
| C | PHE277 |
| C | ARG353 |
| site_id | AE9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 408 |
| Chain | Residue |
| C | ASN307 |
| C | LEU308 |
| C | ALA309 |
| site_id | AF1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 409 |
| Chain | Residue |
| C | TYR317 |
| C | GLY320 |
| C | VAL321 |
| C | LYS325 |
| C | THR326 |
| C | LEU327 |
| C | EDO410 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 410 |
| Chain | Residue |
| C | LEU327 |
| C | GLU347 |
| C | EDO406 |
| C | EDO409 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 411 |
| Chain | Residue |
| C | ALA112 |
| C | TRP141 |
| C | PHE152 |
| C | TYR154 |
| C | LEU155 |
| site_id | AF4 |
| Number of Residues | 9 |
| Details | binding site for residue EDO C 412 |
| Chain | Residue |
| C | VAL214 |
| C | ASP216 |
| C | VAL217 |
| C | SER226 |
| C | VAL227 |
| C | ASN228 |
| C | ILE369 |
| C | ASN372 |
| C | HOH516 |
| site_id | AF5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 413 |
| Chain | Residue |
| C | ASN310 |
| C | ILE348 |
| C | THR349 |
| site_id | AF6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 414 |
| Chain | Residue |
| C | HIS78 |
| C | GLU95 |
| C | TYR96 |
| C | GLY97 |
| site_id | AF7 |
| Number of Residues | 10 |
| Details | binding site for residue B3N D 401 |
| Chain | Residue |
| D | HIS142 |
| D | HIS143 |
| D | GLY151 |
| D | PHE152 |
| D | ASP178 |
| D | HIS180 |
| D | PHE208 |
| D | ASP267 |
| D | TYR306 |
| D | ZN402 |
| site_id | AF8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 402 |
| Chain | Residue |
| D | ASP178 |
| D | HIS180 |
| D | ASP267 |
| D | B3N401 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue K D 403 |
| Chain | Residue |
| D | ASP176 |
| D | ASP178 |
| D | HIS180 |
| D | SER199 |
| D | LEU200 |
| site_id | AG1 |
| Number of Residues | 6 |
| Details | binding site for residue K D 404 |
| Chain | Residue |
| D | PHE189 |
| D | THR192 |
| D | VAL195 |
| D | TYR225 |
| D | HOH502 |
| D | HOH525 |
| site_id | AG2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 405 |
| Chain | Residue |
| D | PRO281 |
| D | TYR317 |
| D | LEU346 |
| D | GLU347 |
| D | ILE348 |
| D | HOH540 |
| site_id | AG3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 406 |
| Chain | Residue |
| D | ARG313 |
| D | TYR340 |
| D | ASP343 |
| D | TYR344 |
| D | VAL345 |
| D | GLU347 |
| D | EDO408 |
| site_id | AG4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 407 |
| Chain | Residue |
| D | TYR18 |
| D | ALA38 |
| D | VAL41 |
| D | HIS42 |
| D | TRP137 |
| D | SER138 |
| D | HOH524 |
| site_id | AG5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 408 |
| Chain | Residue |
| D | ASN310 |
| D | ILE348 |
| D | THR349 |
| D | EDO406 |
| D | HOH515 |
| site_id | AG6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 409 |
| Chain | Residue |
| D | TRP141 |
| D | PHE152 |
| D | CYS153 |
| D | TYR154 |
| D | LEU155 |
| site_id | AG7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 410 |
| Chain | Residue |
| B | GLU23 |
| B | TYR24 |
| D | HIS360 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | HIS143 | |
| B | HIS143 | |
| C | HIS143 | |
| D | HIS143 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | ASP101 | |
| D | ASP101 | |
| D | GLY151 | |
| D | TYR306 | |
| A | GLY151 | |
| A | TYR306 | |
| B | ASP101 | |
| B | GLY151 | |
| B | TYR306 | |
| C | ASP101 | |
| C | GLY151 | |
| C | TYR306 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17721440 |
| Chain | Residue | Details |
| A | ASP178 | |
| D | ASP178 | |
| D | HIS180 | |
| D | ASP267 | |
| A | HIS180 | |
| A | ASP267 | |
| B | ASP178 | |
| B | HIS180 | |
| B | ASP267 | |
| C | ASP178 | |
| C | HIS180 | |
| C | ASP267 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:15242608 |
| Chain | Residue | Details |
| A | SER39 | |
| B | SER39 | |
| C | SER39 | |
| D | SER39 |
