5JCB
Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000226 | biological_process | microtubule cytoskeleton organization |
| A | 0000278 | biological_process | mitotic cell cycle |
| A | 0003924 | molecular_function | GTPase activity |
| A | 0005200 | molecular_function | structural constituent of cytoskeleton |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005856 | cellular_component | cytoskeleton |
| A | 0005874 | cellular_component | microtubule |
| A | 0007017 | biological_process | microtubule-based process |
| A | 0015630 | cellular_component | microtubule cytoskeleton |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000226 | biological_process | microtubule cytoskeleton organization |
| B | 0000278 | biological_process | mitotic cell cycle |
| B | 0003924 | molecular_function | GTPase activity |
| B | 0005200 | molecular_function | structural constituent of cytoskeleton |
| B | 0005515 | molecular_function | protein binding |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005856 | cellular_component | cytoskeleton |
| B | 0005874 | cellular_component | microtubule |
| B | 0007017 | biological_process | microtubule-based process |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000226 | biological_process | microtubule cytoskeleton organization |
| C | 0000278 | biological_process | mitotic cell cycle |
| C | 0003924 | molecular_function | GTPase activity |
| C | 0005200 | molecular_function | structural constituent of cytoskeleton |
| C | 0005525 | molecular_function | GTP binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005856 | cellular_component | cytoskeleton |
| C | 0005874 | cellular_component | microtubule |
| C | 0007017 | biological_process | microtubule-based process |
| C | 0015630 | cellular_component | microtubule cytoskeleton |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000226 | biological_process | microtubule cytoskeleton organization |
| D | 0000278 | biological_process | mitotic cell cycle |
| D | 0003924 | molecular_function | GTPase activity |
| D | 0005200 | molecular_function | structural constituent of cytoskeleton |
| D | 0005515 | molecular_function | protein binding |
| D | 0005525 | molecular_function | GTP binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005856 | cellular_component | cytoskeleton |
| D | 0005874 | cellular_component | microtubule |
| D | 0007017 | biological_process | microtubule-based process |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0031110 | biological_process | regulation of microtubule polymerization or depolymerization |
| F | 0036211 | biological_process | protein modification process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 27 |
| Details | binding site for residue GTP A 501 |
| Chain | Residue |
| A | GLY10 |
| A | GLY143 |
| A | GLY144 |
| A | THR145 |
| A | GLY146 |
| A | VAL177 |
| A | SER178 |
| A | THR179 |
| A | GLU183 |
| A | ASN206 |
| A | TYR224 |
| A | GLN11 |
| A | ASN228 |
| A | ILE231 |
| A | MG502 |
| A | HOH613 |
| A | HOH619 |
| A | HOH652 |
| A | HOH654 |
| B | LYS254 |
| A | ALA12 |
| A | GLN15 |
| A | ASP98 |
| A | ALA99 |
| A | ALA100 |
| A | ASN101 |
| A | SER140 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | GLU71 |
| A | GTP501 |
| A | HOH607 |
| A | HOH619 |
| A | HOH652 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 503 |
| Chain | Residue |
| A | MET1 |
| A | GLU3 |
| A | THR130 |
| A | GLY131 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 504 |
| Chain | Residue |
| A | ASN216 |
| A | ALA273 |
| A | PRO274 |
| A | VAL275 |
| A | ALA294 |
| A | ASN300 |
| A | HOH611 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue IMD A 505 |
| Chain | Residue |
| A | SER287 |
| A | VAL288 |
| A | ARG373 |
| C | ARG308 |
| C | ARG339 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue CA A 506 |
| Chain | Residue |
| A | ASP39 |
| A | THR41 |
| A | GLY44 |
| A | GLU55 |
| A | HOH624 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 507 |
| Chain | Residue |
| A | SER158 |
| A | GLY162 |
| A | GLU196 |
| A | ASP199 |
| A | HOH601 |
| site_id | AC8 |
| Number of Residues | 23 |
| Details | binding site for residue GDP B 501 |
| Chain | Residue |
| B | GLY10 |
| B | GLN11 |
| B | CYS12 |
| B | GLN15 |
| B | SER140 |
| B | GLY143 |
| B | GLY144 |
| B | THR145 |
| B | GLY146 |
| B | PRO173 |
| B | VAL177 |
| B | ASP179 |
| B | GLU183 |
| B | ASN206 |
| B | TYR224 |
| B | ASN228 |
| B | MG502 |
| B | HOH605 |
| B | HOH612 |
| B | HOH621 |
| B | HOH631 |
| B | HOH650 |
| B | HOH669 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | GLN11 |
| B | ASP179 |
| B | GDP501 |
| B | HOH619 |
| B | HOH669 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue NA B 503 |
| Chain | Residue |
| B | GLU110 |
| B | GLU113 |
| C | CA507 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue MES B 504 |
| Chain | Residue |
| B | ARG158 |
| B | PRO162 |
| B | ASP163 |
| B | ARG164 |
| B | ASN197 |
| B | ASP199 |
| B | ARG253 |
| site_id | AD3 |
| Number of Residues | 20 |
| Details | binding site for residue NV4 B 505 |
| Chain | Residue |
| A | VAL181 |
| B | CYS241 |
| B | LEU248 |
| B | ALA250 |
| B | ASP251 |
| B | LYS254 |
| B | LEU255 |
| B | ASN258 |
| B | MET259 |
| B | THR314 |
| B | VAL315 |
| B | ALA316 |
| B | ALA317 |
| B | ASN350 |
| B | LYS352 |
| B | ALA354 |
| B | HOH640 |
| A | ASN101 |
| A | SER178 |
| A | ALA180 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 501 |
| Chain | Residue |
| B | GLY100 |
| B | LYS105 |
| C | THR253 |
| C | THR257 |
| site_id | AD5 |
| Number of Residues | 27 |
| Details | binding site for residue GTP C 502 |
| Chain | Residue |
| C | GLY10 |
| C | GLN11 |
| C | ALA12 |
| C | GLN15 |
| C | ASP98 |
| C | ALA99 |
| C | ALA100 |
| C | ASN101 |
| C | SER140 |
| C | GLY143 |
| C | GLY144 |
| C | THR145 |
| C | GLY146 |
| C | SER178 |
| C | GLU183 |
| C | ASN206 |
| C | TYR224 |
| C | ASN228 |
| C | ILE231 |
| C | MG503 |
| C | HOH615 |
| C | HOH632 |
| C | HOH633 |
| C | HOH652 |
| C | HOH684 |
| C | HOH686 |
| D | LYS254 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 503 |
| Chain | Residue |
| C | GLU71 |
| C | GTP502 |
| C | HOH615 |
| C | HOH633 |
| C | HOH684 |
| site_id | AD7 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 504 |
| Chain | Residue |
| C | SER287 |
| C | VAL288 |
| C | ASP322 |
| C | ASP327 |
| C | ARG373 |
| C | HOH608 |
| C | HOH629 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue PEG C 505 |
| Chain | Residue |
| C | ARG79 |
| C | LEU92 |
| C | ILE93 |
| C | THR94 |
| C | LEU117 |
| C | HOH690 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue NA C 506 |
| Chain | Residue |
| C | ASP39 |
| C | THR41 |
| C | GLY44 |
| C | GLU55 |
| C | HOH641 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue CA C 507 |
| Chain | Residue |
| B | GLU113 |
| B | NA503 |
| C | GLU279 |
| C | TYR282 |
| site_id | AE2 |
| Number of Residues | 1 |
| Details | binding site for residue GOL C 509 |
| Chain | Residue |
| B | ASP120 |
| site_id | AE3 |
| Number of Residues | 17 |
| Details | binding site for residue GDP D 501 |
| Chain | Residue |
| D | GLY10 |
| D | GLN11 |
| D | CYS12 |
| D | GLN15 |
| D | SER140 |
| D | GLY143 |
| D | GLY144 |
| D | THR145 |
| D | GLY146 |
| D | VAL177 |
| D | GLU183 |
| D | ASN206 |
| D | TYR224 |
| D | ASN228 |
| D | MG502 |
| D | HOH608 |
| D | HOH616 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue MG D 502 |
| Chain | Residue |
| D | GLN11 |
| D | ASP179 |
| D | GDP501 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 503 |
| Chain | Residue |
| D | GLY237 |
| D | VAL238 |
| D | THR240 |
| D | CYS241 |
| D | ILE318 |
| D | NV4507 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue GOL D 504 |
| Chain | Residue |
| D | PRO222 |
| D | TYR224 |
| site_id | AE7 |
| Number of Residues | 8 |
| Details | binding site for residue GOL D 505 |
| Chain | Residue |
| C | TRP407 |
| D | ARG158 |
| D | PRO162 |
| D | ASP163 |
| D | ARG164 |
| D | ILE165 |
| D | ASP199 |
| D | ARG253 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 506 |
| Chain | Residue |
| D | PHE296 |
| D | VAL335 |
| D | ASN339 |
| D | HOH627 |
| site_id | AE9 |
| Number of Residues | 22 |
| Details | binding site for residue NV4 D 507 |
| Chain | Residue |
| C | ASN101 |
| C | SER178 |
| C | THR179 |
| C | ALA180 |
| C | VAL181 |
| D | LEU242 |
| D | LEU248 |
| D | ALA250 |
| D | ASP251 |
| D | LYS254 |
| D | LEU255 |
| D | ASN258 |
| D | MET259 |
| D | VAL315 |
| D | ALA317 |
| D | ILE318 |
| D | ASN350 |
| D | LYS352 |
| D | THR353 |
| D | ALA354 |
| D | ILE378 |
| D | MG503 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue MG F 401 |
| Chain | Residue |
| F | ARG222 |
| F | ASP318 |
| F | GLU331 |
| F | ASN333 |
| F | ACP402 |
| site_id | AF2 |
| Number of Residues | 12 |
| Details | binding site for residue ACP F 402 |
| Chain | Residue |
| F | GLN183 |
| F | LYS184 |
| F | LEU186 |
| F | LYS198 |
| F | ASP200 |
| F | HIS239 |
| F | THR241 |
| F | ASN242 |
| F | ILE330 |
| F | GLU331 |
| F | ASN333 |
| F | MG401 |
Functional Information from PROSITE/UniProt
| site_id | PS00227 |
| Number of Residues | 7 |
| Details | TUBULIN Tubulin subunits alpha, beta, and gamma signature. GGGTGSG |
| Chain | Residue | Details |
| A | GLY142-GLY148 | |
| B | GLY142-GLY148 |
| site_id | PS00228 |
| Number of Residues | 4 |
| Details | TUBULIN_B_AUTOREG Tubulin-beta mRNA autoregulation signal. MREI |
| Chain | Residue | Details |
| B | MET1-ILE4 |
| site_id | PS00563 |
| Number of Residues | 10 |
| Details | STATHMIN_1 Stathmin family signature 1. PRRRDpSLEE |
| Chain | Residue | Details |
| E | PRO40-GLU49 |
| site_id | PS01041 |
| Number of Residues | 10 |
| Details | STATHMIN_2 Stathmin family signature 2. AEKREHEREV |
| Chain | Residue | Details |
| E | ALA73-VAL82 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q13509 |
| Chain | Residue | Details |
| B | GLN11 | |
| D | GLY144 | |
| D | THR145 | |
| D | GLY146 | |
| D | ASN206 | |
| D | ASN228 | |
| B | SER140 | |
| B | GLY144 | |
| B | THR145 | |
| B | GLY146 | |
| B | ASN206 | |
| B | ASN228 | |
| D | GLN11 | |
| D | SER140 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P68363 |
| Chain | Residue | Details |
| B | GLU71 | |
| C | GLU71 | |
| C | SER140 | |
| C | GLY144 | |
| C | THR145 | |
| C | THR179 | |
| C | ASN206 | |
| C | ASN228 | |
| D | GLU71 | |
| A | SER140 | |
| A | GLY144 | |
| A | THR145 | |
| A | THR179 | |
| A | ASN206 | |
| A | ASN228 | |
| C | GLN11 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P99024 |
| Chain | Residue | Details |
| B | SER40 | |
| D | SER40 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P99024 |
| Chain | Residue | Details |
| B | LYS60 | |
| D | LYS60 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by CDK1 => ECO:0000250|UniProtKB:Q13885 |
| Chain | Residue | Details |
| B | SER174 | |
| D | SER174 | |
| C | SER48 | |
| C | SER232 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| B | THR287 | |
| B | THR292 | |
| D | THR287 | |
| D | THR292 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| B | ARG320 | |
| D | ARG320 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: 5-glutamyl polyglutamate => ECO:0000250|UniProtKB:Q2T9S0 |
| Chain | Residue | Details |
| B | GLU448 | |
| D | GLU448 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| B | LYS60 | |
| D | LYS60 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P07437 |
| Chain | Residue | Details |
| A | GLU445 | |
| B | LYS326 | |
| D | LYS326 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: 3'-nitrotyrosine => ECO:0000250|UniProtKB:Q71U36 |
| Chain | Residue | Details |
| A | TYR451 | |
| C | TYR451 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P68363 |
| Chain | Residue | Details |
| A | LYS326 | |
| A | LYS370 | |
| C | LYS326 | |
| C | LYS370 |
