Research workbench
Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dgtp
Analyse Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FYD
- Type
- protein + DNA + RNA
- Length
- 1,752 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit a; DNA (5'…
- EC
- 2.7.7.7
- UniProt
- P13382
- Ligands
- DGT
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase alpha catalytic subunit a (EC 2.7.7.7) | protein | 848 | 40% helix, 22% strand | P13382 |
| C, D | DNA (5'- D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*C P*CP*G)-3') | dna | 16 | — | — |
| E, F | DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3') | rna | 12 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, C, E, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.82 | 0.85 | 71 | empty |
| 2 | 646 | 0.81 | 0.86 | 63 | empty |
| 3 | 547 | 0.80 | 0.87 | 46 | empty |
| 4 | 612 | 0.78 | 0.84 | 47 | empty |
| 5 | 449 | 0.74 | 0.83 | 39 | empty |
Interfaces
10 interfaces between chains.
- A–C · 1218 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 1146 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–F · 699 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 695 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–F · 536 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 4FYD · Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP · the same entry in another collection · chain F against F, TM-score 1.00
- P13382 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha catalytic subunit a (P13382) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P13382
- Elsewhere: RCSB PDB 4FYD · PDBe 4FYD · UniProt P13382
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