MolNFT v1 · #153862 · protein
Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase MGM1
6JSJ · Dynamin-like GTPase MGM1, mitochondrial: “Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase MGM1”. X-ray diffraction, 2 ligands (GDP, IOD), 20 pockets (best druggability 0.87). MolNFT v1 #153862 on…
- PDB
- 6JSJ
- Type
- protein
- Length
- 1,868 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-like GTPase MGM1, mitochondrial
- UniProt
- P32266
- Ligands
- GDP, IOD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-like GTPase MGM1, mitochondrial | protein | 625 | 64% helix, 7% strand | P32266 |
| B | Dynamin-like GTPase MGM1, mitochondrial | protein | 624 | 59% helix, 8% strand | P32266 |
| C | Dynamin-like GTPase MGM1, mitochondrial | protein | 619 | 64% helix, 8% strand | P32266 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- IOD · Iodide ion · ion · 25 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.87 | 0.88 | 94 | IOD |
| 2 | 1124 | 0.86 | 0.87 | 104 | IOD |
| 3 | 851 | 0.86 | 0.88 | 82 | IOD |
| 4 | 205 | 0.61 | 0.82 | 32 | GDP |
| 5 | 164 | 0.60 | 0.83 | 19 | IOD |
Interfaces
3 interfaces between chains.
- B–C · 1736 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1657 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1514 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6JSJ · Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1 · the same entry in another collection · chain A against A, TM-score 1.00
- P32266 · AlphaFold monomer V2.0 prediction for dynamin-like GTPase MGM1, mitochondrial (P32266) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P32266
- Elsewhere: RCSB PDB 6JSJ · PDBe 6JSJ · UniProt P32266
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