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Crystal structure of the accessory subunit of murine mitochondrial polymerase gamma
Analyse Crystal structure of the accessory subunit of murine mitochondrial polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G5I
- Type
- protein
- Length
- 1,622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial DNA polymerase accessory subunit
- UniProt
- Q9QZM2
- Ligands
- NA
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mitochondrial DNA polymerase accessory subunit | protein | 405 | 41% helix, 26% strand | Q9QZM2 |
| B | Mitochondrial DNA polymerase accessory subunit | protein | 397 | 43% helix, 27% strand | Q9QZM2 |
| D | Mitochondrial DNA polymerase accessory subunit | protein | 415 | 42% helix, 27% strand | Q9QZM2 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.85 | 0.90 | 39 | empty |
| 2 | 628 | 0.85 | 0.90 | 48 | empty |
| 3 | 1171 | 0.84 | 0.85 | 111 | empty |
| 4 | 706 | 0.82 | 0.86 | 89 | NA |
| 5 | 1058 | 0.80 | 0.82 | 109 | NA |
Interfaces
6 interfaces between chains.
- C–D · 3680 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3462 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 557 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1G5I · Crystal structure of the accessory subunit of murine mitochondrial polymerase gamma · the same entry in another collection · chain D against D, TM-score 1.00
- Q9QZM2 · AlphaFold monomer V2.0 prediction for DNA polymerase subunit gamma-2, mitochondrial… · a predicted model of the same protein · chain B 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 Q9QZM2
- Elsewhere: RCSB PDB 1G5I · PDBe 1G5I · UniProt Q9QZM2
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