Research workbench
MDM12 from K. lactis (1-239), lys residues are uniformly dimethyl modified
Analyse MDM12 from K. lactis (1-239), lys residues are uniformly dimethyl modified in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H5A
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial distribution and morphology protein 12
- UniProt
- Q6CUC3
- Ligands
- 6OU, K
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial distribution and morphology protein 12 | protein | 214 | 26% helix, 39% strand | Q6CUC3 |
| B | Mitochondrial distribution and morphology protein 12 | protein | 213 | 27% helix, 39% strand | Q6CUC3 |
| C | Mitochondrial distribution and morphology protein 12 | protein | 208 | 26% helix, 39% strand | Q6CUC3 |
| D | Mitochondrial distribution and morphology protein 12 | protein | 211 | 25% helix, 40% strand | Q6CUC3 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 4 copies · chains A, D, B, C
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.81 | 0.85 | 59 | 6OU |
| 2 | 601 | 0.81 | 0.85 | 47 | 6OU |
| 3 | 581 | 0.81 | 0.85 | 50 | 6OU |
| 4 | 620 | 0.80 | 0.84 | 51 | 6OU |
| 5 | 620 | 0.68 | 0.77 | 65 | empty |
Interfaces
3 interfaces between chains.
- C–D · 829 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5H5A · Mdm12 from K. lactis (1-239), Lys residues are uniformly dimethyl modified · the same entry in another collection · chain D against D, TM-score 1.00
- Q6CUC3 · AlphaFold monomer V2.0 prediction for mitochondrial distribution and morphology protein… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q6CUC3
- Elsewhere: RCSB PDB 5H5A · PDBe 5H5A · UniProt Q6CUC3
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