Research workbench
Pol domain of POL1 from M. smegmatis
Analyse Pol domain of POL1 from M. smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VDC
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- I7G3P9
- Ligands
- MN
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 497 | 52% helix, 15% strand | I7G3P9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.50 | 0.78 | 20 | empty |
| 2 | 160 | 0.44 | 0.75 | 28 | empty |
| 3 | 136 | 0.44 | 0.76 | 31 | empty |
| 4 | 69 | 0.36 | 0.77 | 12 | empty |
| 5 | 68 | 0.32 | 0.75 | 13 | empty |
Compared structures
- 6VDC · POL domain of Pol1 from M. smegmatis · 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 I7G3P9
- Elsewhere: RCSB PDB 6VDC · PDBe 6VDC · UniProt I7G3P9
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