MolNFT v2 · #216971 · protein + DNA
Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) bound to a primer/template substrate containing three consecutive mismatches
8PPV · DNA polymerase II small subunit: “Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) bound to a primer/template substrate…”. Electron microscopy at 3.02, 2 ligands (MG, ZN), 20 pockets (best druggability 0.82).…
- PDB
- 8PPV
- Type
- protein + DNA
- Length
- 2,409 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.02
- Source
- Pyrococcus abyssi GE5; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase II small subunit; DP2; DNA polymerase sliding clamp; DNA…
- EC
- 2.7.7.7, 3.1.11.1
- UniProt
- Q9V2F3, Q9UYX8
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.02 · 5 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase II small subunit (EC 2.7.7.7, 3.1.11.1) | protein | 447 | 22% helix, 26% strand | Q9V2F3 |
| B | DP2 | protein | 1188 | 39% helix, 15% strand | — |
| C, D, E | DNA polymerase sliding clamp | protein | 246 | 17% helix, 45% strand | Q9UYX8 |
| P | DNA (5'-D(*P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(G7P)P*(PST)P*(PST)P*(PST))-3') | dna | 19 | — | — |
| T | DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.82 | 0.87 | 82 | empty |
| 2 | 78 | 0.76 | 0.97 | 21 | empty |
| 3 | 61 | 0.75 | 0.98 | 18 | empty |
| 4 | 83 | 0.75 | 0.96 | 17 | empty |
| 5 | 68 | 0.74 | 0.98 | 21 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2096 Ų buried · 21 hydrogen bonds · protein-protein
- P–T · 752 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–P · 698 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–E · 698 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 652 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- Q9V2F3 · AlphaFold monomer V2.0 prediction for DNA polymerase II small subunit (Q9V2F3) · 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 Q9V2F3
- Every structure of UniProt Q9UYX8
- Elsewhere: RCSB PDB 8PPV · PDBe 8PPV · UniProt Q9V2F3 · UniProt Q9UYX8
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