5ZBU
Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
Functional Information from GO Data
Chain | GOid | namespace | contents |
B | 0000151 | cellular_component | ubiquitin ligase complex |
B | 0000209 | biological_process | protein polyubiquitination |
B | 0004842 | molecular_function | ubiquitin-protein transferase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005524 | molecular_function | ATP binding |
B | 0005634 | cellular_component | nucleus |
B | 0005654 | cellular_component | nucleoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
B | 0016567 | biological_process | protein ubiquitination |
B | 0016740 | molecular_function | transferase activity |
B | 0019787 | molecular_function | ubiquitin-like protein transferase activity |
B | 0031625 | molecular_function | ubiquitin protein ligase binding |
B | 0032991 | cellular_component | protein-containing complex |
B | 0036211 | biological_process | protein modification process |
B | 0051865 | biological_process | protein autoubiquitination |
B | 0061630 | molecular_function | ubiquitin protein ligase activity |
B | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
B | 0070062 | cellular_component | extracellular exosome |
B | 0070936 | biological_process | protein K48-linked ubiquitination |
C | 0000151 | cellular_component | ubiquitin ligase complex |
C | 0000209 | biological_process | protein polyubiquitination |
C | 0004842 | molecular_function | ubiquitin-protein transferase activity |
C | 0005515 | molecular_function | protein binding |
C | 0005524 | molecular_function | ATP binding |
C | 0005634 | cellular_component | nucleus |
C | 0005654 | cellular_component | nucleoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
C | 0016567 | biological_process | protein ubiquitination |
C | 0016740 | molecular_function | transferase activity |
C | 0019787 | molecular_function | ubiquitin-like protein transferase activity |
C | 0031625 | molecular_function | ubiquitin protein ligase binding |
C | 0032991 | cellular_component | protein-containing complex |
C | 0036211 | biological_process | protein modification process |
C | 0051865 | biological_process | protein autoubiquitination |
C | 0061630 | molecular_function | ubiquitin protein ligase activity |
C | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
C | 0070062 | cellular_component | extracellular exosome |
C | 0070936 | biological_process | protein K48-linked ubiquitination |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | binding site for residue ZN A 1001 |
Chain | Residue |
A | CYS240 |
A | CYS243 |
A | HIS263 |
A | CYS266 |
site_id | AC2 |
Number of Residues | 4 |
Details | binding site for residue ZN A 1002 |
Chain | Residue |
A | CYS258 |
A | HIS260 |
A | CYS278 |
A | CYS281 |
site_id | AC3 |
Number of Residues | 4 |
Details | binding site for residue ZN D 1001 |
Chain | Residue |
D | CYS243 |
D | HIS263 |
D | CYS266 |
D | CYS240 |
site_id | AC4 |
Number of Residues | 4 |
Details | binding site for residue ZN D 1002 |
Chain | Residue |
D | CYS258 |
D | HIS260 |
D | CYS278 |
D | CYS281 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 2 |
Details | SITE: Interacts with activating enzyme |
Chain | Residue | Details |
E | ARG54 | |
E | ARG72 |
site_id | SWS_FT_FI2 |
Number of Residues | 1 |
Details | SITE: Essential for function |
Chain | Residue | Details |
E | HIS68 |
site_id | SWS_FT_FI3 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 |
Chain | Residue | Details |
E | SER65 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
Chain | Residue | Details |
E | THR66 |
site_id | SWS_FT_FI5 |
Number of Residues | 1 |
Details | MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742 |
Chain | Residue | Details |
E | GLY76 |
site_id | SWS_FT_FI6 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 |
Chain | Residue | Details |
E | LYS6 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) |
Chain | Residue | Details |
E | GLY76 |
site_id | SWS_FT_FI8 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 |
Chain | Residue | Details |
E | LYS11 | |
E | LYS48 |
site_id | SWS_FT_FI9 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
Chain | Residue | Details |
E | LYS27 |
site_id | SWS_FT_FI10 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 |
Chain | Residue | Details |
E | LYS29 |
site_id | SWS_FT_FI11 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
Chain | Residue | Details |
E | LYS33 |
site_id | SWS_FT_FI12 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 |
Chain | Residue | Details |
E | LYS63 |