Research workbench
Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin
Analyse Crystal structure of the catalytic core of human DNA polymerase alpha in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q5V
- Type
- protein + DNA + RNA
- Length
- 1,778 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit; RNA primer; DNA template
- EC
- 2.7.7.7
- UniProt
- P09884
- Ligands
- 2ZE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 865 | 39% helix, 22% strand | P09884 |
| B, F | RNA primer | rna | 11 | — | — |
| C, G | DNA template | dna | 13 | — | — |
Ligands and binding sites
- 2ZE · (3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecahydro-8,11a-methanocyclohepta[a]naphthale ne-3,9-diol · ligand · 2 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.82 | 0.83 | 98 | empty |
| 2 | 632 | 0.78 | 0.83 | 58 | empty |
| 3 | 763 | 0.77 | 0.81 | 62 | empty |
| 4 | 843 | 0.73 | 0.78 | 70 | 2ZE |
| 5 | 96 | 0.70 | 0.93 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1776 Ų buried · 25 hydrogen bonds · protein-protein
- E–G · 1124 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 1124 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 784 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 770 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 4Q5V · Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex… · the same entry in another collection · chain G against G, 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 1.00
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 4Q5V · PDBe 4Q5V · UniProt P09884
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