Research workbench
Crystal structure of MDM12-deletion mutant
Analyse Crystal structure of MDM12-deletion mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GYK
- Type
- protein
- Length
- 1,354 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial distribution and morphology protein 12
- UniProt
- Q92328
- Ligands
- PEE
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Mitochondrial distribution and morphology protein 12 | protein | 227 | 26% helix, 39% strand | Q92328 |
| B | Mitochondrial distribution and morphology protein 12 | protein | 223 | 28% helix, 39% strand | Q92328 |
| C | Mitochondrial distribution and morphology protein 12 | protein | 226 | 26% helix, 42% strand | Q92328 |
| E | Mitochondrial distribution and morphology protein 12 | protein | 226 | 28% helix, 39% strand | Q92328 |
| F | Mitochondrial distribution and morphology protein 12 | protein | 225 | 25% helix, 37% strand | Q92328 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.81 | 0.87 | 66 | empty |
| 2 | 648 | 0.81 | 0.84 | 60 | PEE |
| 3 | 1193 | 0.80 | 0.81 | 108 | empty |
| 4 | 449 | 0.79 | 0.86 | 39 | empty |
| 5 | 587 | 0.79 | 0.84 | 55 | PEE |
Interfaces
5 interfaces between chains.
- C–D · 1514 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1496 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 934 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 923 Ų buried · 15 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 Q92328
- Elsewhere: RCSB PDB 5GYK · PDBe 5GYK · UniProt Q92328
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