6SQO

Crystal structure of human MDM2 RING domain homodimer 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

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 501

Chain	Residue
A	CYS438
A	CYS441
A	CYS461
A	CYS464

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 502

Chain	Residue
A	HIS452
A	HIS457
A	CYS475
A	CYS478

---

site_id	AC3
Number of Residues	1
Details	binding site for residue CL A 503

Chain	Residue
A	ILE485

---

site_id	AC4
Number of Residues	4
Details	binding site for residue CL B 201

Chain	Residue
A	HOH622
B	ALA2
B	LEU3
B	LYS4

---

site_id	AC5
Number of Residues	2
Details	binding site for residue NO3 B 202

Chain	Residue
B	ARG136
B	GLU140

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN D 501

Chain	Residue
D	CYS438
D	CYS441
D	CYS461
D	CYS464

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN D 502

Chain	Residue
D	HIS452
D	HIS457
D	CYS475
D	CYS478

---

site_id	AC8
Number of Residues	1
Details	binding site for residue CL D 503

Chain	Residue
D	ILE485

---

site_id	AC9
Number of Residues	4
Details	binding site for residue CL E 201

Chain	Residue
E	ALA2
E	LEU3
E	LYS4
E	HOH422

---

site_id	AD1
Number of Residues	5
Details	binding site for residue NO3 E 202

Chain	Residue
E	LYS85
E	ARG90
E	LYS133
E	ARG136
E	HOH322

---

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

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	82
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	14
Details	Motif: {"description":"Nucleolar localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
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_FI4
Number of Residues	150
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
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_FI8
Number of Residues	2
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
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_FI11
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	4
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_FI13
Number of Residues	2
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_FI14
Number of Residues	2
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_FI15
Number of Residues	2
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_FI16
Number of Residues	2
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

---