Research workbench
Crystal structure of the computationally designed chemically disruptable heterodimer LD6-MDM2
Analyse Crystal structure of the computationally designed chemically disruptable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AYE
- Type
- protein
- Length
- 205 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 11 of E3 ubiquitin-protein ligase MDM2; THIOL:DISULFIDE interchange protein dsbd
- EC
- 2.3.2.27, 1.8.1.8
- UniProt
- Q00987, Q328D2
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 11 of E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 86 | 45% helix, 12% strand | Q00987 |
| B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 119 | 37% helix, 18% strand | Q328D2 |
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 | 133 | 0.43 | 0.75 | 24 | empty |
| 2 | 76 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7AYE · Crystal structure of the computationally designed chemically disruptable heterodimer… · the same entry in another collection · chain A against A, TM-score 1.00
- Q328D2 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsbd (Q328D2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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
- Every structure of UniProt Q328D2
- Elsewhere: RCSB PDB 7AYE · PDBe 7AYE · UniProt Q00987 · UniProt Q328D2
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