Research workbench
Bst DNA polymerase I pre-chemistry (N) structure
Analyse Bst DNA polymerase I pre-chemistry (N) structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DSW
- Type
- protein + DNA
- Length
- 601 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*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.72
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*G)-3') | dna | 9 | — | — |
| T | DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)- 3') | dna | 15 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 56% helix, 13% strand | E1C9K5 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.72 | 0.76 | 76 | SO4, MG |
| 2 | 146 | 0.71 | 0.91 | 22 | empty |
| 3 | 335 | 0.67 | 0.82 | 45 | empty |
| 4 | 183 | 0.46 | 0.74 | 20 | empty |
| 5 | 135 | 0.45 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1457 Ų buried · 32 hydrogen bonds · protein-nucleic
- P–A · 781 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 442 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DSW · Bst DNA polymerase I pre-chemistry (n) 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 6DSW · PDBe 6DSW · UniProt E1C9K5
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