MolNFT v1 · #114953 · protein + DNA
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma
5C53 · DNA polymerase subunit gamma-1: “Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase…”. X-ray diffraction, 3 ligands (4Y3, DOC, MG), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 5C53
- Type
- protein + DNA
- Length
- 1,751 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase subunit gamma-1; Pol gamma B; DNA (26-mer); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- P54098
- Ligands
- 4Y3, DOC, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase subunit gamma-1 (EC 2.7.7.7) | protein | 983 | 34% helix, 8% strand | P54098 |
| B | Pol gamma B | protein | 363 | 33% helix, 27% strand | — |
| C | Pol gamma B | protein | 358 | 32% helix, 25% strand | — |
| 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 | 21 | — | — |
Ligands and binding sites
- 4Y3 · [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.86 | 0.87 | 88 | empty |
| 2 | 1028 | 0.84 | 0.85 | 89 | empty |
| 3 | 885 | 0.83 | 0.85 | 120 | empty |
| 4 | 1095 | 0.78 | 0.80 | 110 | empty |
| 5 | 422 | 0.77 | 0.86 | 56 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2248 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2076 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 1420 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 1040 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–P · 646 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5C53 · Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human… · the same entry in another collection · chain B against B, TM-score 1.00
- 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
- Elsewhere: RCSB PDB 5C53 · PDBe 5C53 · UniProt P54098
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