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Crystal structure of DNA polymerase alpha catalytic core in complex with dctp and TEMPLATE/PRIMER having T-C mismatch at the post- insertion site
Analyse Crystal structure of DNA polymerase alpha catalytic core in complex with dctp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N2M
- Type
- protein + DNA + RNA
- Length
- 889 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit; RNA (5'-R(*GP*CP*CP*UP*GP*GP*AP*GP*CP*GP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- P09884
- Ligands
- DCP, ZN, MG, K, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 865 | 40% helix, 23% strand | P09884 |
| B | RNA (5'-R(*GP*CP*CP*UP*GP*GP*AP*GP*CP*GP*C)-3') | rna | 11 | — | — |
| C | DNA (5'-D(*AP*T*AP*GP*TP*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
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
- K · Potassium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.78 | 0.81 | 52 | SO4 |
| 2 | 1072 | 0.76 | 0.79 | 85 | DCP, ZN |
| 3 | 145 | 0.68 | 0.89 | 27 | empty |
| 4 | 402 | 0.66 | 0.79 | 52 | empty |
| 5 | 152 | 0.54 | 0.80 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1094 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 759 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 518 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 7N2M · Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and… · 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 0.98
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 P09884
- Elsewhere: RCSB PDB 7N2M · PDBe 7N2M · UniProt P09884
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