MolNFT v1 · #146797 · protein + DNA
Bst DNA polymerase I post-chemistry (N+2) structure
6DSV · DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'): “Bst DNA polymerase I post-chemistry (N+2) structure”. X-ray diffraction, 2 ligands (MG, SO4), 9 pockets (best druggability 0.79). MolNFT v1 #146797 on GenesisL1: 3D structure…
- PDB
- 6DSV
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'); DNA polymerase I; DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- MG, SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3') | dna | 11 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 56% helix, 13% strand | E1C9K5 |
| T | DNA (5'-D(P*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.79 | 0.94 | 28 | empty |
| 2 | 320 | 0.72 | 0.86 | 37 | empty |
| 3 | 817 | 0.68 | 0.75 | 62 | MG, SO4 |
| 4 | 312 | 0.63 | 0.80 | 43 | empty |
| 5 | 254 | 0.60 | 0.79 | 29 | empty |
Interfaces
3 interfaces between chains.
- P–A · 785 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–T · 757 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 525 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DSV · Bst DNA polymerase I post-chemistry (n+2) structure · the same entry in another collection · chain P against P, 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 E1C9K5
- Elsewhere: RCSB PDB 6DSV · PDBe 6DSV · UniProt E1C9K5
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