Research workbench
Crystal structure of human mitochondrial DNA polymerase holoenzyme
Analyse Crystal structure of human mitochondrial DNA polymerase holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKM
- Type
- protein
- Length
- 3,689 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase subunit gamma-1; DNA polymerase subunit gamma-2
- EC
- 2.7.7.7
- UniProt
- P54098, Q9UHN1
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase subunit gamma-1 (EC 2.7.7.7) | protein | 1093 | 37% helix, 3% strand | P54098 |
| B, E | DNA polymerase subunit gamma-2 (EC 2.7.7.7) | protein | 355 | 30% helix, 11% strand | Q9UHN1 |
| C, F | DNA polymerase subunit gamma-2 (EC 2.7.7.7) | protein | 396 | 36% helix, 10% strand | Q9UHN1 |
| D | DNA polymerase subunit gamma-1 (EC 2.7.7.7) | protein | 1094 | 37% helix, 3% strand | P54098 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.88 | 0.90 | 134 | empty |
| 2 | 1186 | 0.88 | 0.90 | 135 | empty |
| 3 | 986 | 0.88 | 0.90 | 112 | empty |
| 4 | 1115 | 0.86 | 0.87 | 121 | empty |
| 5 | 431 | 0.85 | 0.93 | 66 | empty |
Interfaces
8 interfaces between chains.
- A–C · 2178 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2153 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2073 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1938 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 113 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3IKM · Crystal structure of human mitochondrial DNA polymerase holoenzyme · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UHN1 · 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 0.96
- P54098 · AlphaFold monomer V2.0 prediction for DNA polymerase subunit gamma-1 (P54098) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P54098
- Every structure of UniProt Q9UHN1
- Elsewhere: RCSB PDB 3IKM · PDBe 3IKM · UniProt P54098 · UniProt Q9UHN1
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