Research workbench
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma
Analyse Probing the structural and molecular basis of nucleotide selectivity by human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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