MolNFT v1 · #167194 · protein + DNA
Pol domain of POL1 from M. smegmatis complex with DNA primer-template and dntp
6VDD · DNA polymerase I: “Pol domain of POL1 from M. smegmatis complex with DNA primer-template and dntp”. X-ray diffraction, 2 ligands (DCT, MG), 17 pockets (best druggability 0.76). MolNFT v1 #167194 on GenesisL1: 3D structure, binding…
- PDB
- 6VDD
- Type
- protein + DNA
- Length
- 1,183 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- I7G3P9
- Ligands
- DCT, MG
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 567 | 54% helix, 13% strand | I7G3P9 |
| B, E | DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 14 | — | — |
| D | DNA polymerase I (EC 2.7.7.7) | protein | 567 | 53% helix, 13% strand | I7G3P9 |
| F | DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.76 | 0.80 | 84 | empty |
| 2 | 427 | 0.76 | 0.85 | 51 | empty |
| 3 | 394 | 0.75 | 0.86 | 43 | empty |
| 4 | 1145 | 0.70 | 0.75 | 67 | DCT, MG |
| 5 | 776 | 0.67 | 0.75 | 66 | DCT, MG |
Interfaces
7 interfaces between chains.
- A–C · 1044 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–F · 918 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 823 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 814 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–D · 762 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VDD · POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP · 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 6VDD · PDBe 6VDD · UniProt I7G3P9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.