MolNFT v1 · #122177 · protein
D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)
5IHE · DNA polymerase II small subunit: “D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)”. X-ray diffraction, 4 ligands (D5M, CA, FE), 12 pockets (best druggability 0.67). MolNFT v1 #122177 on GenesisL1: 3D…
- PDB
- 5IHE
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase II small subunit
- EC
- 2.7.7.7
- UniProt
- Q9V2F3
- Ligands
- D5M, CA, FE, ZN
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase II small subunit (EC 2.7.7.7) | protein | 440 | 22% helix, 30% strand | Q9V2F3 |
| B | DNA polymerase II small subunit (EC 2.7.7.7) | protein | 442 | 22% helix, 30% strand | Q9V2F3 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.67 | 0.77 | 63 | empty |
| 2 | 410 | 0.66 | 0.79 | 45 | CA |
| 3 | 313 | 0.64 | 0.80 | 42 | D5M |
| 4 | 336 | 0.62 | 0.79 | 46 | D5M, EDO |
| 5 | 91 | 0.56 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 757 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IHE · D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
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
- Elsewhere: RCSB PDB 5IHE · PDBe 5IHE · UniProt Q9V2F3
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