Research workbench
D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451 proof-reading deficient variant
Analyse D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HMF
- 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, 3.1.11.1
- UniProt
- Q9V2F3
- Ligands
- FE, ZN, CA
- Pockets
- 11 · best druggability 0.75
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, 3.1.11.1) | protein | 440 | 22% helix, 30% strand | Q9V2F3 |
| B | DNA polymerase II small subunit (EC 2.7.7.7, 3.1.11.1) | protein | 442 | 22% helix, 30% strand | Q9V2F3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.75 | 0.78 | 96 | CA |
| 2 | 371 | 0.67 | 0.80 | 46 | CAC |
| 3 | 364 | 0.65 | 0.80 | 48 | CAC |
| 4 | 97 | 0.57 | 0.86 | 18 | empty |
| 5 | 147 | 0.42 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6HMF · D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451… · 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 6HMF · PDBe 6HMF · UniProt Q9V2F3
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