1XT9
Crystal Structure of Den1 in complex with Nedd8
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000338 | biological_process | protein deneddylation |
| A | 0005515 | molecular_function | protein binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0006508 | biological_process | proteolysis |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0016579 | biological_process | protein deubiquitination |
| A | 0019784 | molecular_function | deNEDDylase activity |
| A | 0043687 | biological_process | post-translational protein modification |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| B | 0006508 | biological_process | proteolysis |
| B | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| B | 0008104 | biological_process | protein localization |
| B | 0009653 | biological_process | anatomical structure morphogenesis |
| B | 0016567 | biological_process | protein ubiquitination |
| B | 0019941 | biological_process | modification-dependent protein catabolic process |
| B | 0030162 | biological_process | regulation of proteolysis |
| B | 0031386 | molecular_function | protein tag activity |
| B | 0031625 | molecular_function | ubiquitin protein ligase binding |
| B | 0036211 | biological_process | protein modification process |
| B | 0045116 | biological_process | protein neddylation |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0098978 | cellular_component | glutamatergic synapse |
| B | 0150052 | biological_process | regulation of postsynapse assembly |
Functional Information from PROSITE/UniProt
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD |
| Chain | Residue | Details |
| B | LYS27-ASP52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | SITE: Interaction with UBE1C => ECO:0000269|PubMed:14690597 |
| Chain | Residue | Details |
| B | LEU8 | |
| B | ILE44 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | MOD_RES: (Microbial infection) Deamidated glutamine => ECO:0000269|PubMed:20688984, ECO:0000269|PubMed:21903097, ECO:0000269|PubMed:23175788, ECO:0000269|PubMed:23589306, ECO:0000269|PubMed:26632597 |
| Chain | Residue | Details |
| B | GLN40 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P29595 |
| Chain | Residue | Details |
| B | LYS48 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) |
| Chain | Residue | Details |
| B | GLY76 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 5 |
| Details | Annotated By Reference To The Literature 2bkr |
| Chain | Residue | Details |
| A | TRP103 | |
| A | HIS102 | |
| A | ASP119 | |
| A | TRP26 | |
| A | CYS163 |
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 820 |
| Chain | Residue | Details |
| A | TRP26 | electrostatic stabiliser |
| A | HIS102 | proton acceptor, proton donor |
| A | TRP103 | electrostatic stabiliser |
| A | ASP119 | electrostatic stabiliser |
| A | CYS163 | nucleofuge, nucleophile, proton acceptor, proton donor |
