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Crystal structure of an archaebacterial DNA polymerase D.TOK. deposition of second native structure at 2.4 ångström
Analyse Crystal structure of an archaebacterial DNA polymerase D.TOK. deposition of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D5A
- Type
- protein
- Length
- 733 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (DNA polymerase)
- EC
- 2.7.7.7
- UniProt
- Q7SIG8
- Ligands
- MG, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (DNA polymerase) (EC 2.7.7.7) | protein | 733 | 38% helix, 22% strand | Q7SIG8 |
Ligands and binding sites
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 | 954 | 0.75 | 0.78 | 72 | SO4, MG |
| 2 | 351 | 0.60 | 0.77 | 37 | empty |
| 3 | 271 | 0.59 | 0.78 | 26 | SO4 |
| 4 | 219 | 0.56 | 0.79 | 30 | SO4 |
| 5 | 151 | 0.44 | 0.75 | 23 | SO4 |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1D5A · Crystal structure of an archaebacterial DNA polymerase D.TOK. deposition of second native… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7SIG8
- Elsewhere: RCSB PDB 1D5A · PDBe 1D5A · UniProt Q7SIG8
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