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Crystal structure of DNA-directed DNA polymerase
Analyse Crystal structure of DNA-directed DNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JGU
- Type
- protein
- Length
- 711 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P61875
- Ligands
- MN
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 711 | 36% helix, 20% strand | P61875 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.65 | 0.78 | 43 | MN |
| 2 | 388 | 0.64 | 0.78 | 49 | empty |
| 3 | 289 | 0.59 | 0.77 | 28 | empty |
| 4 | 84 | 0.44 | 0.80 | 14 | empty |
| 5 | 141 | 0.44 | 0.76 | 27 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 P61875
- Elsewhere: RCSB PDB 2JGU · PDBe 2JGU · UniProt P61875
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