MolNFT v1 · #143185 · protein + DNA
Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an DNA-primed DNA template and dctp
6AS7 · DNA polymerase alpha catalytic subunit: “Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an DNA-primed…”. X-ray diffraction, 3 ligands (DCP, MG, CO), 10 pockets (best druggability 0.74).…
- PDB
- 6AS7
- Type
- protein + DNA
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit; DNA (5'-D(*GP*CP*CP*TP*GP*GP*AP*GP*CP*GP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- P09884
- Ligands
- DCP, MG, CO
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 870 | 38% helix, 22% strand | P09884 |
| B | DNA (5'-D(*GP*CP*CP*TP*GP*GP*AP*GP*CP*GP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*AP*GP*GP*CP*GP*CP*TP*CP*CP*AP*GP*GP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.74 | 0.82 | 40 | empty |
| 2 | 525 | 0.66 | 0.77 | 48 | empty |
| 3 | 369 | 0.65 | 0.79 | 49 | DCP, MG |
| 4 | 364 | 0.62 | 0.77 | 37 | empty |
| 5 | 372 | 0.61 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 991 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 597 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 503 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 6AS7 · Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P09884 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha catalytic subunit (P09884) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P09884
- Elsewhere: RCSB PDB 6AS7 · PDBe 6AS7 · UniProt P09884
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