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Crystal structure of the cytosolic domain of human MID51
Analyse Crystal structure of the cytosolic domain of human MID51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NXV
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial dynamic protein MID51
- UniProt
- Q9NQG6
- Ligands
- GDP, SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mitochondrial dynamic protein MID51 | protein | 330 | 46% helix, 17% strand | Q9NQG6 |
| C | Mitochondrial dynamic protein MID51 | protein | 337 | 48% helix, 18% strand | Q9NQG6 |
| D | Mitochondrial dynamic protein MID51 | protein | 331 | 47% helix, 17% strand | Q9NQG6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.76 | 0.86 | 32 | empty |
| 2 | 750 | 0.74 | 0.79 | 79 | GDP |
| 3 | 703 | 0.74 | 0.79 | 71 | GDP |
| 4 | 424 | 0.73 | 0.83 | 41 | empty |
| 5 | 706 | 0.72 | 0.79 | 75 | GDP |
Interfaces
5 interfaces between chains.
- B–D · 646 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 638 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 107 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4NXV · Crystal structure of the cytosolic domain of human MiD51 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQG6 · AlphaFold monomer V2.0 prediction for mitochondrial dynamics protein MID51 (Q9NQG6) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9NQG6
- Elsewhere: RCSB PDB 4NXV · PDBe 4NXV · UniProt Q9NQG6
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