5THV
Crystal Structure of G305A 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 | 0031078 | molecular_function | histone H3K14 deacetylase activity, hydrolytic mechanism |
| A | 0031397 | biological_process | negative regulation of protein ubiquitination |
| A | 0031647 | biological_process | regulation of protein stability |
| A | 0032129 | molecular_function | histone H3K9 deacetylase activity, hydrolytic mechanism |
| A | 0032204 | biological_process | regulation of telomere maintenance |
| A | 0033558 | molecular_function | protein lysine deacetylase activity |
| A | 0034739 | molecular_function | histone H4K16 deacetylase activity, hydrolytic mechanism |
| A | 0040029 | biological_process | epigenetic regulation of gene expression |
| A | 0042903 | molecular_function | tubulin 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 | 0140937 | molecular_function | histone H4K12 deacetylase activity, hydrolytic mechanism |
| A | 0160008 | molecular_function | protein decrotonylase activity |
| A | 0160009 | molecular_function | histone decrotonylase activity |
| A | 0180032 | molecular_function | histone H4K5 deacetylase activity, hydrolytic mechanism |
| A | 0180033 | molecular_function | histone H4K8 deacetylase activity, hydrolytic mechanism |
| A | 1990162 | molecular_function | histone H3K4 deacetylase activity, hydrolytic mechanism |
| 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 | 0031078 | molecular_function | histone H3K14 deacetylase activity, hydrolytic mechanism |
| B | 0031397 | biological_process | negative regulation of protein ubiquitination |
| B | 0031647 | biological_process | regulation of protein stability |
| B | 0032129 | molecular_function | histone H3K9 deacetylase activity, hydrolytic mechanism |
| B | 0032204 | biological_process | regulation of telomere maintenance |
| B | 0033558 | molecular_function | protein lysine deacetylase activity |
| B | 0034739 | molecular_function | histone H4K16 deacetylase activity, hydrolytic mechanism |
| B | 0040029 | biological_process | epigenetic regulation of gene expression |
| B | 0042903 | molecular_function | tubulin 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 | 0140937 | molecular_function | histone H4K12 deacetylase activity, hydrolytic mechanism |
| B | 0160008 | molecular_function | protein decrotonylase activity |
| B | 0160009 | molecular_function | histone decrotonylase activity |
| B | 0180032 | molecular_function | histone H4K5 deacetylase activity, hydrolytic mechanism |
| B | 0180033 | molecular_function | histone H4K8 deacetylase activity, hydrolytic mechanism |
| B | 1990162 | molecular_function | histone H3K4 deacetylase activity, hydrolytic mechanism |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| A | B3N404 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue K A 402 |
| Chain | Residue |
| A | ASP176 |
| A | ASP178 |
| A | HIS180 |
| A | SER199 |
| A | LEU200 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue K A 403 |
| Chain | Residue |
| A | PHE189 |
| A | THR192 |
| A | VAL195 |
| A | TYR225 |
| A | HOH519 |
| A | HOH630 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | binding site for residue B3N A 404 |
| Chain | Residue |
| A | HIS142 |
| A | HIS143 |
| A | PHE152 |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| A | GLY304 |
| A | TYR306 |
| A | ZN401 |
| A | EDO416 |
| A | HOH543 |
| B | ILE34 |
| B | PHE152 |
| B | PRO273 |
| B | TYR306 |
| B | B3N404 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | PRO281 |
| A | VAL282 |
| A | TYR317 |
| A | LEU346 |
| A | GLU347 |
| A | ILE348 |
| A | HOH505 |
| A | HOH551 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | ALA188 |
| A | HOH528 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | VAL61 |
| A | SER63 |
| A | HIS360 |
| A | GLN363 |
| A | HOH641 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | LYS132 |
| A | LEU292 |
| A | GLN295 |
| A | LEU296 |
| A | EDO412 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | ALA68 |
| A | PHE70 |
| A | HIS71 |
| A | HOH504 |
| A | HOH516 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | LYS374 |
| A | HIS375 |
| A | VAL376 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 411 |
| Chain | Residue |
| A | TYR317 |
| A | THR326 |
| A | LEU327 |
| A | SER329 |
| A | GLU347 |
| A | HOH551 |
| A | HOH568 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 412 |
| Chain | Residue |
| A | GLN293 |
| A | VAL321 |
| A | ILE322 |
| A | EDO408 |
| A | HOH512 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 413 |
| Chain | Residue |
| A | PHE208 |
| A | PRO209 |
| A | GLY210 |
| A | HOH518 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 414 |
| Chain | Residue |
| A | GLN236 |
| A | ASP237 |
| A | THR280 |
| A | PRO350 |
| A | HOH502 |
| A | HOH525 |
| A | HOH586 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 415 |
| Chain | Residue |
| A | TYR18 |
| A | ALA38 |
| A | VAL41 |
| A | HIS42 |
| A | SER138 |
| A | EDO418 |
| A | HOH511 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 416 |
| Chain | Residue |
| A | TRP141 |
| A | HIS142 |
| A | GLY151 |
| A | CYS153 |
| A | GLY304 |
| A | TYR306 |
| A | B3N404 |
| A | HOH642 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 417 |
| Chain | Residue |
| A | TYR154 |
| A | LEU155 |
| A | TRP141 |
| A | PHE152 |
| site_id | AD9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 418 |
| Chain | Residue |
| A | ARG37 |
| A | ALA38 |
| A | TRP137 |
| A | SER138 |
| A | TRP315 |
| A | EDO415 |
| A | HOH501 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | B3N404 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue K B 402 |
| Chain | Residue |
| B | ASP176 |
| B | ASP178 |
| B | HIS180 |
| B | SER199 |
| B | LEU200 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue K B 403 |
| Chain | Residue |
| B | PHE189 |
| B | THR192 |
| B | VAL195 |
| B | TYR225 |
| B | HOH534 |
| B | HOH631 |
| site_id | AE4 |
| Number of Residues | 16 |
| Details | binding site for residue B3N B 404 |
| Chain | Residue |
| A | LYS33 |
| A | ILE34 |
| A | PRO273 |
| A | TYR306 |
| A | B3N404 |
| B | HIS142 |
| B | HIS143 |
| B | PHE152 |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | GLY304 |
| B | TYR306 |
| B | ZN401 |
| B | HOH551 |
| B | HOH638 |
| site_id | AE5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | ALA188 |
| B | HOH509 |
| B | HOH559 |
| site_id | AE6 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | PRO230 |
| B | ILE231 |
| B | GLN232 |
| B | ASN357 |
| B | ARG361 |
| B | ILE362 |
| B | ILE365 |
| B | EDO407 |
| B | HOH511 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | PHE203 |
| B | ASP213 |
| B | ARG361 |
| B | EDO406 |
| site_id | AE8 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | PHE207 |
| B | PHE208 |
| B | PRO209 |
| B | GLY210 |
| B | EDO415 |
| B | HOH503 |
| B | HOH627 |
| site_id | AE9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| B | PRO281 |
| B | VAL282 |
| B | TYR317 |
| B | LEU346 |
| B | GLU347 |
| B | ILE348 |
| B | HOH524 |
| B | HOH588 |
| site_id | AF1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 410 |
| Chain | Residue |
| A | CYS275 |
| A | ARG353 |
| B | LYS202 |
| B | SER204 |
| B | ASP233 |
| B | HOH518 |
| site_id | AF2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 411 |
| Chain | Residue |
| B | GLU65 |
| B | ALA68 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 412 |
| Chain | Residue |
| B | VAL214 |
| B | SER215 |
| B | TYR368 |
| B | ASN372 |
| site_id | AF4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 413 |
| Chain | Residue |
| B | TYR111 |
| B | TRP141 |
| B | PHE152 |
| B | CYS153 |
| B | TYR154 |
| B | LEU155 |
| site_id | AF5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 414 |
| Chain | Residue |
| B | VAL133 |
| B | LEU292 |
| B | GLN295 |
| B | LEU296 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 415 |
| Chain | Residue |
| B | SER150 |
| B | PHE208 |
| B | PRO209 |
| B | EDO408 |
| B | HOH510 |
| B | HOH578 |
| site_id | AF7 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 416 |
| Chain | Residue |
| B | THR326 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | HIS143 | |
| B | HIS143 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | ASP101 | |
| A | GLY151 | |
| A | TYR306 | |
| B | ASP101 | |
| B | GLY151 | |
| B | TYR306 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17721440 |
| Chain | Residue | Details |
| A | ASP178 | |
| A | HIS180 | |
| A | ASP267 | |
| B | ASP178 | |
| B | HIS180 | |
| B | ASP267 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:15242608 |
| Chain | Residue | Details |
| A | SER39 | |
| B | SER39 |
