MolNFT v1 · #114952 · protein + DNA
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma
5C52 · DNA polymerase subunit gamma-1: “Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase…”. X-ray diffraction, 2 ligands (1RY, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5C52
- Type
- protein + DNA
- Length
- 1,752 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase subunit gamma-1; DNA polymerase subunit gamma-2, mitochondrial; DNA…
- EC
- 2.7.7.7
- UniProt
- P54098, Q9UHN1
- Ligands
- 1RY, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase subunit gamma-1 (EC 2.7.7.7) | protein | 983 | 33% helix, 8% strand | P54098 |
| B | DNA polymerase subunit gamma-2, mitochondrial (EC 2.7.7.7) | protein | 363 | 35% helix, 26% strand | Q9UHN1 |
| C | DNA polymerase subunit gamma-2, mitochondrial (EC 2.7.7.7) | protein | 358 | 30% helix, 25% strand | Q9UHN1 |
| T | DNA (26-mer) | dna | 26 | — | — |
| P | DNA (5'- D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)- 3') | dna | 22 | — | — |
Ligands and binding sites
- 1RY · [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 695 | 0.84 | 0.87 | 56 | empty |
| 2 | 1163 | 0.82 | 0.83 | 95 | empty |
| 3 | 797 | 0.80 | 0.83 | 87 | empty |
| 4 | 1070 | 0.79 | 0.80 | 104 | empty |
| 5 | 965 | 0.78 | 0.80 | 96 | 1RY, MG |
Interfaces
6 interfaces between chains.
- A–B · 2341 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2094 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 1420 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 1041 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–P · 779 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5C52 · Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human… · the same entry in another collection · chain P against P, 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 C against A, TM-score 0.97
- 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 0.86
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 5C52 · PDBe 5C52 · UniProt P54098 · UniProt Q9UHN1
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