MolNFT v1 · #120376 · protein
Crystal structure of MDM12
5GYD · Mitochondrial distribution and morphology protein 12: “Crystal structure of MDM12”. X-ray diffraction, 1 ligand (PEE), 10 pockets (best druggability 0.82). MolNFT v1 #120376 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5GYD
- Type
- protein
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial distribution and morphology protein 12
- UniProt
- Q92328
- Ligands
- PEE
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial distribution and morphology protein 12 | protein | 227 | 29% helix, 41% strand | Q92328 |
| B | Mitochondrial distribution and morphology protein 12 | protein | 224 | 25% helix, 41% strand | Q92328 |
| C | Mitochondrial distribution and morphology protein 12 | protein | 228 | 28% helix, 40% strand | Q92328 |
| D | Mitochondrial distribution and morphology protein 12 | protein | 222 | 28% helix, 41% strand | Q92328 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.82 | 0.87 | 46 | PEE |
| 2 | 437 | 0.80 | 0.88 | 54 | PEE |
| 3 | 584 | 0.80 | 0.85 | 58 | PEE |
| 4 | 402 | 0.78 | 0.87 | 63 | PEE |
| 5 | 90 | 0.41 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1399 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1394 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 11 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 5GYD · PDBe 5GYD · UniProt Q92328
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