MolNFT v1 · #140733 · protein
Crystal structure of MDM12-MMM1 complex
5YK7 · Maintenance of mitochondrial morphology protein 1: “Crystal structure of MDM12-MMM1 complex”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.86). MolNFT v1 #140733 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YK7
- Type
- protein
- Length
- 834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maintenance of mitochondrial morphology protein 1; Mitochondrial distribution and…
- UniProt
- C5DRQ1, Q92328
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maintenance of mitochondrial morphology protein 1 | protein | 221 | 30% helix, 33% strand | C5DRQ1 |
| B | Mitochondrial distribution and morphology protein 12 | protein | 197 | 27% helix, 40% strand | Q92328 |
| C | Maintenance of mitochondrial morphology protein 1 | protein | 220 | 29% helix, 32% strand | C5DRQ1 |
| D | Mitochondrial distribution and morphology protein 12 | protein | 196 | 30% helix, 39% strand | Q92328 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.86 | 0.90 | 84 | empty |
| 2 | 1030 | 0.83 | 0.83 | 71 | PO4 |
| 3 | 344 | 0.82 | 0.91 | 37 | empty |
| 4 | 1174 | 0.81 | 0.81 | 67 | empty |
| 5 | 241 | 0.75 | 0.88 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2754 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1048 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YK7 · Crystal Structure of Mdm12-Mmm1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- C5DRQ1 · AlphaFold monomer V2.0 prediction for maintenance of mitochondrial morphology protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q92328 · AlphaFold monomer V2.0 prediction for mitochondrial distribution and morphology protein… · a predicted model of the same protein · chain D against A, TM-score 0.85
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 C5DRQ1
- Every structure of UniProt Q92328
- Elsewhere: RCSB PDB 5YK7 · PDBe 5YK7 · UniProt C5DRQ1 · UniProt Q92328
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