Research workbench
Cryo-EM Structure of DNA Polymerase Delta Holoenzyme
Analyse Cryo-EM Structure of DNA Polymerase Delta Holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P1H
- Type
- protein + DNA
- Length
- 1,566 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase delta catalytic subunit; DNA polymerase delta small subunit; DNA…
- EC
- 2.7.7.7
- UniProt
- P15436, P46957, P47110
- Ligands
- SF4, DCP, CA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.2 · 5 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase delta catalytic subunit (EC 2.7.7.7) | protein | 959 | 36% helix, 19% strand | P15436 |
| B | DNA polymerase delta small subunit (EC 2.7.7.7) | protein | 469 | 20% helix, 21% strand | P46957 |
| C | DNA polymerase delta subunit 3 | protein | 111 | 21% helix, 15% strand | P47110 |
| P | DNA (30-mer) | dna | 12 | — | — |
| T | DNA (30-mer) | dna | 15 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 5 copies · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.80 | 0.86 | 76 | CA |
| 2 | 255 | 0.78 | 0.91 | 37 | empty |
| 3 | 121 | 0.70 | 0.91 | 22 | empty |
| 4 | 404 | 0.66 | 0.80 | 45 | empty |
| 5 | 141 | 0.66 | 0.88 | 24 | DCP, CA |
Interfaces
5 interfaces between chains.
- B–C · 2590 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2452 Ų buried · 26 hydrogen bonds · protein-protein
- A–T · 1270 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 703 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 529 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 6P1H · Cryo-EM structure of DNA polymerase delta holoenzyme · the same entry in another collection · chain T against T, TM-score 1.00
- P15436 · AlphaFold monomer V2.0 prediction for DNA polymerase delta catalytic subunit (P15436) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P46957 · AlphaFold monomer V2.0 prediction for DNA polymerase delta small subunit (P46957) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P47110 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 3 (P47110) · a predicted model of the same protein · chain C against A, TM-score 0.75
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 P15436
- Every structure of UniProt P46957
- Every structure of UniProt P47110
- Elsewhere: RCSB PDB 6P1H · PDBe 6P1H · UniProt P15436 · UniProt P46957 · UniProt P47110
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