3Q9C
Crystal Structure of H159A APAH complexed with N8-acetylspermidine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004407 | molecular_function | histone deacetylase activity |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| A | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| B | 0004407 | molecular_function | histone deacetylase activity |
| B | 0006338 | biological_process | chromatin remodeling |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| B | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| C | 0004407 | molecular_function | histone deacetylase activity |
| C | 0006338 | biological_process | chromatin remodeling |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| C | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| D | 0004407 | molecular_function | histone deacetylase activity |
| D | 0006338 | biological_process | chromatin remodeling |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| D | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| E | 0004407 | molecular_function | histone deacetylase activity |
| E | 0006338 | biological_process | chromatin remodeling |
| E | 0016787 | molecular_function | hydrolase activity |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| E | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| F | 0004407 | molecular_function | histone deacetylase activity |
| F | 0006338 | biological_process | chromatin remodeling |
| F | 0016787 | molecular_function | hydrolase activity |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| F | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| G | 0004407 | molecular_function | histone deacetylase activity |
| G | 0006338 | biological_process | chromatin remodeling |
| G | 0016787 | molecular_function | hydrolase activity |
| G | 0046872 | molecular_function | metal ion binding |
| G | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| G | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| H | 0004407 | molecular_function | histone deacetylase activity |
| H | 0006338 | biological_process | chromatin remodeling |
| H | 0016787 | molecular_function | hydrolase activity |
| H | 0046872 | molecular_function | metal ion binding |
| H | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| H | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| I | 0004407 | molecular_function | histone deacetylase activity |
| I | 0006338 | biological_process | chromatin remodeling |
| I | 0016787 | molecular_function | hydrolase activity |
| I | 0046872 | molecular_function | metal ion binding |
| I | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| I | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| J | 0004407 | molecular_function | histone deacetylase activity |
| J | 0006338 | biological_process | chromatin remodeling |
| J | 0016787 | molecular_function | hydrolase activity |
| J | 0046872 | molecular_function | metal ion binding |
| J | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| J | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| K | 0004407 | molecular_function | histone deacetylase activity |
| K | 0006338 | biological_process | chromatin remodeling |
| K | 0016787 | molecular_function | hydrolase activity |
| K | 0046872 | molecular_function | metal ion binding |
| K | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| K | 0047611 | molecular_function | acetylspermidine deacetylase activity |
| L | 0004407 | molecular_function | histone deacetylase activity |
| L | 0006338 | biological_process | chromatin remodeling |
| L | 0016787 | molecular_function | hydrolase activity |
| L | 0046872 | molecular_function | metal ion binding |
| L | 0047609 | molecular_function | acetylputrescine deacetylase activity |
| L | 0047611 | molecular_function | acetylspermidine deacetylase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE Q9C A 401 |
| Chain | Residue |
| A | TYR19 |
| A | PHE225 |
| A | GLY321 |
| A | TYR323 |
| A | ZN343 |
| A | HOH1000 |
| I | GLU106 |
| A | GLU117 |
| A | PRO156 |
| A | HIS158 |
| A | GLY167 |
| A | TYR168 |
| A | CYS169 |
| A | ASP195 |
| A | HIS197 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 342 |
| Chain | Residue |
| A | ASP193 |
| A | ASP195 |
| A | HIS197 |
| A | SER216 |
| A | LEU217 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 343 |
| Chain | Residue |
| A | ASP195 |
| A | HIS197 |
| A | ASP284 |
| A | TYR323 |
| A | Q9C401 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 344 |
| Chain | Residue |
| A | PHE206 |
| A | ARG209 |
| A | VAL212 |
| A | THR243 |
| A | HOH353 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE Q9C B 402 |
| Chain | Residue |
| B | TYR19 |
| B | GLU117 |
| B | PRO156 |
| B | HIS158 |
| B | GLY167 |
| B | TYR168 |
| B | CYS169 |
| B | ASP195 |
| B | HIS197 |
| B | PHE225 |
| B | TYR323 |
| B | ZN343 |
| B | HOH565 |
| B | HOH1449 |
| F | GLU106 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 342 |
| Chain | Residue |
| B | ASP193 |
| B | ASP195 |
| B | HIS197 |
| B | SER216 |
| B | LEU217 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 343 |
| Chain | Residue |
| B | ASP195 |
| B | HIS197 |
| B | ASP284 |
| B | Q9C402 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 344 |
| Chain | Residue |
| B | PHE206 |
| B | ARG209 |
| B | VAL212 |
| B | THR243 |
| B | HOH352 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE Q9C C 403 |
| Chain | Residue |
| C | TYR19 |
| C | GLU117 |
| C | HIS158 |
| C | GLY167 |
| C | TYR168 |
| C | ASP195 |
| C | HIS197 |
| C | PHE225 |
| C | TYR323 |
| C | ZN343 |
| C | HOH578 |
| C | HOH1084 |
| K | GLU106 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K C 342 |
| Chain | Residue |
| C | ASP193 |
| C | ASP195 |
| C | HIS197 |
| C | SER216 |
| C | LEU217 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 343 |
| Chain | Residue |
| C | ASP195 |
| C | HIS197 |
| C | ASP284 |
| C | Q9C403 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA C 344 |
| Chain | Residue |
| C | PHE206 |
| C | ARG209 |
| C | VAL212 |
| C | THR243 |
| C | HOH351 |
| site_id | BC4 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE Q9C D 404 |
| Chain | Residue |
| D | GLU117 |
| D | PRO156 |
| D | HIS158 |
| D | GLY167 |
| D | TYR168 |
| D | ASP195 |
| D | HIS197 |
| D | PHE225 |
| D | GLY321 |
| D | TYR323 |
| D | ZN343 |
| D | HOH1003 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K D 342 |
| Chain | Residue |
| D | ASP195 |
| D | HIS197 |
| D | SER216 |
| D | LEU217 |
| D | ASP193 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 343 |
| Chain | Residue |
| D | ASP195 |
| D | HIS197 |
| D | ASP284 |
| D | Q9C404 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA D 344 |
| Chain | Residue |
| D | PHE206 |
| D | ARG209 |
| D | VAL212 |
| D | THR243 |
| D | HOH351 |
| site_id | BC8 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE Q9C E 405 |
| Chain | Residue |
| E | TYR19 |
| E | GLU117 |
| E | PRO156 |
| E | HIS158 |
| E | GLY167 |
| E | TYR168 |
| E | CYS169 |
| E | ASP195 |
| E | HIS197 |
| E | PHE225 |
| E | GLY321 |
| E | TYR323 |
| E | ZN343 |
| E | HOH569 |
| H | TYR83 |
| H | GLU106 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K E 342 |
| Chain | Residue |
| E | ASP193 |
| E | ASP195 |
| E | HIS197 |
| E | SER216 |
| E | LEU217 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN E 343 |
| Chain | Residue |
| E | ASP195 |
| E | HIS197 |
| E | ASP284 |
| E | Q9C405 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA E 344 |
| Chain | Residue |
| E | PHE206 |
| E | ARG209 |
| E | VAL212 |
| E | THR243 |
| E | HOH348 |
| site_id | CC3 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE Q9C F 406 |
| Chain | Residue |
| B | TYR83 |
| F | GLU117 |
| F | PRO156 |
| F | HIS158 |
| F | GLY167 |
| F | TYR168 |
| F | CYS169 |
| F | ASP195 |
| F | HIS197 |
| F | PHE225 |
| F | GLY321 |
| F | TYR323 |
| F | ZN343 |
| F | HOH573 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K F 342 |
| Chain | Residue |
| F | ASP193 |
| F | ASP195 |
| F | HIS197 |
| F | SER216 |
| F | LEU217 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN F 343 |
| Chain | Residue |
| F | ASP195 |
| F | HIS197 |
| F | ASP284 |
| F | Q9C406 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA F 344 |
| Chain | Residue |
| F | PHE206 |
| F | ARG209 |
| F | VAL212 |
| F | THR243 |
| F | HOH1031 |
| site_id | CC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE Q9C G 407 |
| Chain | Residue |
| G | TYR19 |
| G | GLU117 |
| G | PRO156 |
| G | HIS158 |
| G | GLY167 |
| G | TYR168 |
| G | CYS169 |
| G | ASP195 |
| G | HIS197 |
| G | PHE225 |
| G | GLY321 |
| G | TYR323 |
| G | ZN343 |
| G | HOH1083 |
| G | HOH1759 |
| L | GLU106 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K G 342 |
| Chain | Residue |
| G | ASP193 |
| G | ASP195 |
| G | HIS197 |
| G | SER216 |
| G | LEU217 |
| site_id | CC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN G 343 |
| Chain | Residue |
| G | ASP195 |
| G | HIS197 |
| G | ASP284 |
| G | Q9C407 |
| site_id | DC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA G 344 |
| Chain | Residue |
| G | PHE206 |
| G | ARG209 |
| G | VAL212 |
| G | THR243 |
| G | HOH347 |
| site_id | DC2 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE Q9C H 408 |
| Chain | Residue |
| E | GLU106 |
| H | TYR19 |
| H | GLU117 |
| H | PRO156 |
| H | HIS158 |
| H | GLY167 |
| H | TYR168 |
| H | CYS169 |
| H | ASP195 |
| H | HIS197 |
| H | PHE225 |
| H | GLY321 |
| H | TYR323 |
| H | ZN343 |
| H | HOH556 |
| H | HOH990 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K H 342 |
| Chain | Residue |
| H | ASP193 |
| H | ASP195 |
| H | HIS197 |
| H | SER216 |
| H | LEU217 |
| site_id | DC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN H 343 |
| Chain | Residue |
| H | ASP195 |
| H | HIS197 |
| H | ASP284 |
| H | TYR323 |
| H | Q9C408 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA H 344 |
| Chain | Residue |
| H | PHE206 |
| H | ARG209 |
| H | VAL212 |
| H | THR243 |
| H | HOH381 |
| site_id | DC6 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE Q9C I 409 |
| Chain | Residue |
| A | GLU106 |
| I | TYR19 |
| I | GLU117 |
| I | PRO156 |
| I | HIS158 |
| I | GLY167 |
| I | TYR168 |
| I | CYS169 |
| I | ASP195 |
| I | HIS197 |
| I | PHE225 |
| I | ASP284 |
| I | GLY321 |
| I | TYR323 |
| I | ZN343 |
| I | HOH558 |
| I | HOH559 |
| site_id | DC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K I 342 |
| Chain | Residue |
| I | ASP193 |
| I | ASP195 |
| I | HIS197 |
| I | SER216 |
| I | LEU217 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN I 343 |
| Chain | Residue |
| I | ASP195 |
| I | HIS197 |
| I | ASP284 |
| I | Q9C409 |
| site_id | DC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA I 344 |
| Chain | Residue |
| I | PHE206 |
| I | ARG209 |
| I | VAL212 |
| I | THR243 |
| I | HOH402 |
| site_id | EC1 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE Q9C J 410 |
| Chain | Residue |
| D | GLU106 |
| J | TYR19 |
| J | GLU117 |
| J | PRO156 |
| J | HIS158 |
| J | GLY167 |
| J | TYR168 |
| J | CYS169 |
| J | ASP195 |
| J | HIS197 |
| J | PHE225 |
| J | GLY321 |
| J | TYR323 |
| J | ZN343 |
| J | HOH555 |
| J | HOH575 |
| site_id | EC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K J 342 |
| Chain | Residue |
| J | ASP193 |
| J | ASP195 |
| J | HIS197 |
| J | SER216 |
| J | LEU217 |
| site_id | EC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN J 343 |
| Chain | Residue |
| J | ASP195 |
| J | HIS197 |
| J | ASP284 |
| J | Q9C410 |
| site_id | EC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA J 344 |
| Chain | Residue |
| J | PHE206 |
| J | ARG209 |
| J | VAL212 |
| J | THR243 |
| J | HOH363 |
| site_id | EC5 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE Q9C K 411 |
| Chain | Residue |
| C | GLU106 |
| K | TYR19 |
| K | GLU117 |
| K | PRO156 |
| K | HIS158 |
| K | GLY167 |
| K | TYR168 |
| K | ASP195 |
| K | HIS197 |
| K | PHE225 |
| K | ASP284 |
| K | GLY321 |
| K | TYR323 |
| K | ZN343 |
| K | HOH561 |
| K | HOH579 |
| site_id | EC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K K 342 |
| Chain | Residue |
| K | ASP193 |
| K | ASP195 |
| K | HIS197 |
| K | SER216 |
| K | LEU217 |
| site_id | EC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN K 343 |
| Chain | Residue |
| K | ASP195 |
| K | HIS197 |
| K | ASP284 |
| K | Q9C411 |
| site_id | EC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA K 344 |
| Chain | Residue |
| K | PHE206 |
| K | ARG209 |
| K | VAL212 |
| K | THR243 |
| K | HOH355 |
| site_id | EC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE Q9C L 412 |
| Chain | Residue |
| G | TYR83 |
| L | TYR19 |
| L | GLU117 |
| L | PRO156 |
| L | HIS158 |
| L | GLY167 |
| L | TYR168 |
| L | CYS169 |
| L | HIS197 |
| L | PHE225 |
| L | TYR323 |
| L | ZN343 |
| L | HOH1002 |
| site_id | FC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K L 342 |
| Chain | Residue |
| L | ASP193 |
| L | ASP195 |
| L | HIS197 |
| L | SER216 |
| L | LEU217 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN L 343 |
| Chain | Residue |
| L | ASP195 |
| L | HIS197 |
| L | ASP284 |
| L | Q9C412 |
| site_id | FC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA L 344 |
| Chain | Residue |
| L | PHE206 |
| L | ARG209 |
| L | VAL212 |
| L | THR243 |
| L | HOH1032 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000305|PubMed:21268586, ECO:0000305|PubMed:26200446 |
| Chain | Residue | Details |
| A | ALA159 | |
| J | ALA159 | |
| K | ALA159 | |
| L | ALA159 | |
| B | ALA159 | |
| C | ALA159 | |
| D | ALA159 | |
| E | ALA159 | |
| F | ALA159 | |
| G | ALA159 | |
| H | ALA159 | |
| I | ALA159 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 36 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21268586, ECO:0007744|PDB:3Q9E |
| Chain | Residue | Details |
| A | TYR19 | |
| D | TYR19 | |
| D | GLU117 | |
| D | TYR323 | |
| E | TYR19 | |
| E | GLU117 | |
| E | TYR323 | |
| F | TYR19 | |
| F | GLU117 | |
| F | TYR323 | |
| G | TYR19 | |
| A | GLU117 | |
| G | GLU117 | |
| G | TYR323 | |
| H | TYR19 | |
| H | GLU117 | |
| H | TYR323 | |
| I | TYR19 | |
| I | GLU117 | |
| I | TYR323 | |
| J | TYR19 | |
| J | GLU117 | |
| A | TYR323 | |
| J | TYR323 | |
| K | TYR19 | |
| K | GLU117 | |
| K | TYR323 | |
| L | TYR19 | |
| L | GLU117 | |
| L | TYR323 | |
| B | TYR19 | |
| B | GLU117 | |
| B | TYR323 | |
| C | TYR19 | |
| C | GLU117 | |
| C | TYR323 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21268586, ECO:0007744|PDB:3Q9C |
| Chain | Residue | Details |
| A | GLU106 | |
| J | GLU106 | |
| K | GLU106 | |
| L | GLU106 | |
| B | GLU106 | |
| C | GLU106 | |
| D | GLU106 | |
| E | GLU106 | |
| F | GLU106 | |
| G | GLU106 | |
| H | GLU106 | |
| I | GLU106 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 36 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21268586, ECO:0000269|PubMed:26200446, ECO:0007744|PDB:3Q9B, ECO:0007744|PDB:3Q9E |
| Chain | Residue | Details |
| A | ASP195 | |
| D | ASP195 | |
| D | HIS197 | |
| D | ASP284 | |
| E | ASP195 | |
| E | HIS197 | |
| E | ASP284 | |
| F | ASP195 | |
| F | HIS197 | |
| F | ASP284 | |
| G | ASP195 | |
| A | HIS197 | |
| G | HIS197 | |
| G | ASP284 | |
| H | ASP195 | |
| H | HIS197 | |
| H | ASP284 | |
| I | ASP195 | |
| I | HIS197 | |
| I | ASP284 | |
| J | ASP195 | |
| J | HIS197 | |
| A | ASP284 | |
| J | ASP284 | |
| K | ASP195 | |
| K | HIS197 | |
| K | ASP284 | |
| L | ASP195 | |
| L | HIS197 | |
| L | ASP284 | |
| B | ASP195 | |
| B | HIS197 | |
| B | ASP284 | |
| C | ASP195 | |
| C | HIS197 | |
| C | ASP284 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | SITE: Polarizes the scissile carbonyl of the substrate => ECO:0000305|PubMed:21268586 |
| Chain | Residue | Details |
| A | TYR323 | |
| J | TYR323 | |
| K | TYR323 | |
| L | TYR323 | |
| B | TYR323 | |
| C | TYR323 | |
| D | TYR323 | |
| E | TYR323 | |
| F | TYR323 | |
| G | TYR323 | |
| H | TYR323 | |
| I | TYR323 |
