6SQR
Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005634 | cellular_component | nucleus |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0043066 | biological_process | negative regulation of apoptotic process |
| A | 0051726 | biological_process | regulation of cell cycle |
| A | 0061630 | molecular_function | ubiquitin protein ligase activity |
| B | 0000166 | molecular_function | nucleotide binding |
| 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 | 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 |
| D | 0005634 | cellular_component | nucleus |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0043066 | biological_process | negative regulation of apoptotic process |
| D | 0051726 | biological_process | regulation of cell cycle |
| D | 0061630 | molecular_function | ubiquitin protein ligase activity |
| E | 0000166 | molecular_function | nucleotide binding |
| E | 0000209 | biological_process | protein polyubiquitination |
| E | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| E | 0016567 | biological_process | protein ubiquitination |
| E | 0016740 | molecular_function | transferase activity |
| E | 0032991 | cellular_component | protein-containing complex |
| E | 0036211 | biological_process | protein modification process |
| E | 0051865 | biological_process | protein autoubiquitination |
| E | 0061630 | molecular_function | ubiquitin protein ligase activity |
| E | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| E | 0070062 | cellular_component | extracellular exosome |
| E | 0070936 | biological_process | protein K48-linked ubiquitination |
| G | 0005634 | cellular_component | nucleus |
| G | 0042802 | molecular_function | identical protein binding |
| G | 0043066 | biological_process | negative regulation of apoptotic process |
| G | 0051726 | biological_process | regulation of cell cycle |
| G | 0061630 | molecular_function | ubiquitin protein ligase activity |
| H | 0000166 | molecular_function | nucleotide binding |
| H | 0000209 | biological_process | protein polyubiquitination |
| H | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| H | 0005515 | molecular_function | protein binding |
| H | 0005524 | molecular_function | ATP binding |
| H | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005829 | cellular_component | cytosol |
| H | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| H | 0016567 | biological_process | protein ubiquitination |
| H | 0016740 | molecular_function | transferase activity |
| H | 0032991 | cellular_component | protein-containing complex |
| H | 0036211 | biological_process | protein modification process |
| H | 0051865 | biological_process | protein autoubiquitination |
| H | 0061630 | molecular_function | ubiquitin protein ligase activity |
| H | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| H | 0070062 | cellular_component | extracellular exosome |
| H | 0070936 | biological_process | protein K48-linked ubiquitination |
| J | 0005634 | cellular_component | nucleus |
| J | 0042802 | molecular_function | identical protein binding |
| J | 0043066 | biological_process | negative regulation of apoptotic process |
| J | 0051726 | biological_process | regulation of cell cycle |
| J | 0061630 | molecular_function | ubiquitin protein ligase activity |
| K | 0000166 | molecular_function | nucleotide binding |
| K | 0000209 | biological_process | protein polyubiquitination |
| K | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| K | 0005515 | molecular_function | protein binding |
| K | 0005524 | molecular_function | ATP binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005654 | cellular_component | nucleoplasm |
| K | 0005829 | cellular_component | cytosol |
| K | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| K | 0016567 | biological_process | protein ubiquitination |
| K | 0016740 | molecular_function | transferase activity |
| K | 0032991 | cellular_component | protein-containing complex |
| K | 0036211 | biological_process | protein modification process |
| K | 0051865 | biological_process | protein autoubiquitination |
| K | 0061630 | molecular_function | ubiquitin protein ligase activity |
| K | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| K | 0070062 | cellular_component | extracellular exosome |
| K | 0070936 | biological_process | protein K48-linked ubiquitination |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 501 |
| Chain | Residue |
| A | ASN433 |
| A | GLU436 |
| A | VAL439 |
| A | LYS446 |
| A | HOH617 |
| C | THR9 |
| D | PRO491 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 502 |
| Chain | Residue |
| A | CYS461 |
| A | CYS464 |
| A | CYS438 |
| A | CYS441 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 503 |
| Chain | Residue |
| A | HIS452 |
| A | HIS457 |
| A | CYS475 |
| A | CYS478 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 201 |
| Chain | Residue |
| A | HOH605 |
| B | ALA96 |
| B | THR98 |
| C | THR9 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 501 |
| Chain | Residue |
| B | ALA19 |
| B | GLN20 |
| B | HOH313 |
| D | LYS469 |
| D | ASN472 |
| D | LYS473 |
| D | ILE482 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 502 |
| Chain | Residue |
| C | ALA46 |
| C | HOH108 |
| D | ASN472 |
| D | HOH617 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | binding site for residue NO3 D 503 |
| Chain | Residue |
| D | ARG444 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 504 |
| Chain | Residue |
| D | CYS438 |
| D | CYS441 |
| D | CYS461 |
| D | CYS464 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 505 |
| Chain | Residue |
| D | HIS452 |
| D | HIS457 |
| D | CYS475 |
| D | CYS478 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO G 501 |
| Chain | Residue |
| G | ASN433 |
| G | GLU436 |
| G | LYS446 |
| I | THR9 |
| J | PRO491 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO G 502 |
| Chain | Residue |
| G | ASN447 |
| G | LEU487 |
| G | THR488 |
| G | TYR489 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN G 503 |
| Chain | Residue |
| G | CYS438 |
| G | CYS441 |
| G | CYS461 |
| G | CYS464 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN G 504 |
| Chain | Residue |
| G | HIS452 |
| G | HIS457 |
| G | CYS475 |
| G | CYS478 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue NO3 H 201 |
| Chain | Residue |
| G | VAL439 |
| H | ARG5 |
| H | ALA96 |
| H | THR98 |
| I | THR9 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO I 101 |
| Chain | Residue |
| H | GLN20 |
| H | LEU104 |
| I | PHE45 |
| I | ALA46 |
| I | GLY47 |
| I | HIS68 |
| I | HOH207 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue NO3 I 102 |
| Chain | Residue |
| I | LYS27 |
| I | GLN49 |
| I | LEU50 |
| I | GLU51 |
| I | ASP52 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO J 501 |
| Chain | Residue |
| I | GLU34 |
| J | TYR489 |
| J | PHE490 |
| J | HOH602 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO J 502 |
| Chain | Residue |
| G | PRO491 |
| J | ASN433 |
| J | GLU436 |
| J | LYS446 |
| J | HOH604 |
| L | THR9 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue ZN J 503 |
| Chain | Residue |
| J | CYS438 |
| J | CYS441 |
| J | ARG444 |
| J | CYS461 |
| J | CYS464 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN J 504 |
| Chain | Residue |
| J | HIS452 |
| J | HIS457 |
| J | CYS475 |
| J | CYS478 |
| site_id | AE3 |
| Number of Residues | 8 |
| Details | binding site for residue EDO K 201 |
| Chain | Residue |
| K | HOH316 |
| K | PHE69 |
| K | THR70 |
| K | THR71 |
| K | ARG72 |
| K | SER80 |
| K | ASN81 |
| K | GLY82 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO K 202 |
| Chain | Residue |
| G | HIS452 |
| G | GLY453 |
| G | GLN480 |
| K | PHE51 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO K 203 |
| Chain | Residue |
| J | HOH612 |
| K | ALA96 |
| K | THR98 |
| L | LEU8 |
| L | THR9 |
Functional Information from PROSITE/UniProt
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| C | LYS27-ASP52 | |
| I | LYS27-ASP52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 164 |
| Details | Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 28 |
| Details | Motif: {"description":"Nucleolar localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Phosphoserine; by ATM","evidences":[{"source":"UniProtKB","id":"Q00987","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 225 |
| Details | Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | Site: {"description":"Interacts with activating enzyme"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 3 |
| Details | Site: {"description":"Essential for function"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 3 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 6 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 6 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 3 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 3 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 3 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 3 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 75 |
| Details | Domain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
