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 | 0008233 | molecular_function | peptidase activity |
| A | 0008234 | molecular_function | cysteine-type peptidase activity |
| A | 0016579 | biological_process | protein deubiquitination |
| A | 0016787 | molecular_function | hydrolase activity |
| 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 | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006508 | biological_process | proteolysis |
| B | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| 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 | 0072757 | biological_process | cellular response to camptothecin |
| B | 0098794 | cellular_component | postsynapse |
| 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 | Active site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Nucleophile"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Region: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
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 |
