Research workbench
Bst DNA polymerase I TNA/DNA binary complex
Analyse Bst DNA polymerase I TNA/DNA binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MU5
- Type
- protein + DNA
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- TG, TFT, FA2, TC, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3') | dna | 10 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 578 | 55% helix, 13% strand | E1C9K5 |
Ligands and binding sites
- TG · 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one · ligand · 4 copies · chains A, P
- TFT · (L)-alpha-threofuranosyl-thymine-3'-monophosphate · ligand · 3 copies · chains A, P
- FA2 · 5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate · ligand · 3 copies · chains P, A
- TC · 4-azanyl-1-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$L^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one · ligand · 3 copies · chains P, A
- SO4 · Sulfate ion · ion · 7 copies · chains P, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.68 | 0.84 | 38 | empty |
| 2 | 617 | 0.65 | 0.75 | 44 | SO4 |
| 3 | 224 | 0.59 | 0.80 | 27 | empty |
| 4 | 110 | 0.45 | 0.78 | 24 | empty |
| 5 | 164 | 0.41 | 0.73 | 25 | FA2 |
Interfaces
1 interface between chains.
- P–A · 839 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 6MU5 · Bst DNA polymerase I TNA/DNA binary complex · 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 6MU5 · PDBe 6MU5 · UniProt E1C9K5
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