MolNFT v1 · #110458 · protein
Crystal structure of human MDM2-RPL11
4XXB · 60S ribosomal protein L11: “Crystal structure of human MDM2-RPL11”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.60). MolNFT v1 #110458 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XXB
- Type
- protein
- Length
- 193 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60S ribosomal protein L11; E3 ubiquitin-protein ligase MDM2
- UniProt
- P62913, Q00987
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 60S ribosomal protein L11 | protein | 151 | 32% helix, 29% strand | P62913 |
| B | E3 ubiquitin-protein ligase MDM2 | protein | 42 | 7% helix, 14% strand | Q00987 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · chains A, B
- BME · Beta-mercaptoethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.60 | 0.77 | 45 | IMD, BME, ZN |
| 2 | 76 | 0.30 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1186 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 P62913
- Every structure of UniProt Q00987
- Elsewhere: RCSB PDB 4XXB · PDBe 4XXB · UniProt P62913 · UniProt Q00987
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