MolNFT v2 · #160951 · protein + DNA
Cryo-EM Structure of DNA Polymerase Delta Holoenzyme
6P1H: “Cryo-EM Structure of DNA Polymerase Delta Holoenzyme”. Electron microscopy at 3.2, 3 ligands (SF4, DCP, CA). MolNFT v2 #160951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
- UniProt
- P15436, P46957, P47110
- Ligands
- SF4, DCP, CA
Structure
electron microscopy · resolution 3.2 · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 959 | — | P15436 |
| B | — | protein | 469 | — | P46957 |
| C | — | protein | 111 | — | P47110 |
| P | — | dna | 12 | — | — |
| T | — | 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, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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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