MolNFT v1 · #164214 · protein
Crystal structure of cat MDM2-S429E ring domain homodimer
6SQP · E3 ubiquitin-protein ligase MDM2: “Crystal structure of cat MDM2-S429E ring domain homodimer”. X-ray diffraction, 3 ligands (ZN, CL, NO3), 2 pockets (best druggability 0.38). MolNFT v1 #164214 on GenesisL1: 3D structure, binding…
- PDB
- 6SQP
- Type
- protein
- Length
- 264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 2.3.2.27
- UniProt
- Q7YRZ8
- Ligands
- ZN, CL, NO3
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 63 | 21% helix, 22% strand | Q7YRZ8 |
| B, D | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 68 | 19% helix, 21% strand | Q7YRZ8 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 65 | 18% helix, 22% strand | Q7YRZ8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
- NO3 · Nitrate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.38 | 0.74 | 27 | empty |
| 2 | 67 | 0.33 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1347 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1185 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 280 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6SQP · Crystal structure of Cat MDM2-S429E RING domain homodimer · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.90
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
- Elsewhere: RCSB PDB 6SQP · PDBe 6SQP · UniProt Q7YRZ8
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