MolNFT v1 · #167195 · protein
Full-length M. smegmatis POL1
6VDE · DNA polymerase I: “Full-length M. smegmatis POL1”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.82). MolNFT v1 #167195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VDE
- Type
- protein
- Length
- 1,720 residues
- Chains
- 2
- 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
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase I (EC 2.7.7.7) | protein | 860 | 45% helix, 12% strand | I7G3P9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.82 | 0.87 | 71 | empty |
| 2 | 664 | 0.80 | 0.85 | 88 | empty |
| 3 | 704 | 0.74 | 0.80 | 72 | empty |
| 4 | 400 | 0.68 | 0.81 | 50 | empty |
| 5 | 304 | 0.68 | 0.83 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 781 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6VDE · Full-length M. smegmatis Pol1 · 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 6VDE · PDBe 6VDE · UniProt I7G3P9
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