MolNFT v1 · #164216 · protein

Crystal structure of cat phospho-SER429 MDM2 ring domain bound to UBCH5B-ub

6SQS · E3 ubiquitin-protein ligase MDM2: “Crystal structure of cat phospho-SER429 MDM2 ring domain bound to UBCH5B-ub”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.64). MolNFT v1 #164216 on GenesisL1: 3D structure…

PDB: 6SQS
Type: protein
Length: 574 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase MDM2; Ubiquitin-conjugating enzyme E2 D2; Ubiquitin-40S…
EC: 2.3.2.27, 2.3.2.23, 2.3.2.24
UniProt: Q7YRZ8, P62837, J3QTR3
Ligands: ZN
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	64	20% helix, 22% strand	Q7YRZ8
B, E	Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24)	protein	146	36% helix, 19% strand	P62837
C, F	Ubiquitin-40S ribosomal protein S27A	protein	77	23% helix, 36% strand	J3QTR3

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	312	0.64	0.80	44	empty
2	148	0.58	0.83	27	empty
3	158	0.51	0.79	21	empty
4	165	0.50	0.78	22	empty
5	90	0.35	0.75	22	empty

Interfaces

9 interfaces between chains.

A–D · 1389 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 864 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 849 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 570 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 527 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 isopeptide, 2 modified (isopeptide, phosphorylation).

Compared structures

6SQS · Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub · the same entry in another collection · chain F against F, TM-score 1.00
P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q7YRZ8 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (Q7YRZ8) · a predicted model of the same protein · chain A against A, TM-score 0.89

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q7YRZ8
Every structure of UniProt P62837
Every structure of UniProt J3QTR3
Elsewhere: RCSB PDB 6SQS · PDBe 6SQS · UniProt Q7YRZ8 · UniProt P62837 · UniProt J3QTR3

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