Research workbench
Crystal structure of open bacillus fragment DNA polymerase bound to DNA and dttp
Analyse Crystal structure of open bacillus fragment DNA polymerase bound to DNA and dttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YFU
- Type
- protein + DNA
- Length
- 1,202 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; Primer DNA; Template DNA
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- TTP, GLC, FRU, SO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 579 | 55% helix, 13% strand | E1C9K5 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | E1C9K5 |
| B, E | Primer DNA | dna | 9 | — | — |
| C | Template DNA | dna | 11 | — | — |
| F | Template DNA | dna | 14 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.72 | 0.79 | 52 | empty |
| 2 | 143 | 0.71 | 0.91 | 23 | empty |
| 3 | 992 | 0.70 | 0.75 | 74 | TTP |
| 4 | 383 | 0.69 | 0.82 | 46 | GLC, FRU |
| 5 | 513 | 0.69 | 0.79 | 55 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1299 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 1183 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–E · 826 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 817 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 673 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact, nucleotide modification).
Compared structures
- 4YFU · Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP · 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 E1C9K5
- Elsewhere: RCSB PDB 4YFU · PDBe 4YFU · UniProt E1C9K5
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