MolNFT v1 · #138774 · protein
Green fluorescent protein linked mtide-02 inhibitor in complex with MDM2
5WTS: “Green fluorescent protein linked mtide-02 inhibitor in complex with MDM2”. X-ray diffraction, 2 ligands (CRO, PO4), 3 pockets (best druggability 0.79). MolNFT v1 #138774 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WTS
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein linked mtide-02; E3 ubiquitin-protein ligase MDM2
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- CRO, PO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein linked mtide-02 | protein | 349 | 11% helix, 48% strand | — |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 96 | 41% helix, 17% strand | Q00987 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.98 | 29 | CRO |
| 2 | 282 | 0.51 | 0.74 | 33 | GOL |
| 3 | 61 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 821 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
- 5WTS · Green fluorescent protein linked MTide-02 inhibitor in complex with mdm2 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q00987
- Elsewhere: RCSB PDB 5WTS · PDBe 5WTS · UniProt Q00987
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