MolNFT v1 · #111074 · protein + DNA
Crystal structure of open bacillus fragment DNA polymerase bound to DNA and dttp
4YFU: “Crystal structure of open bacillus fragment DNA polymerase bound to DNA and dttp”. X-ray diffraction, 4 ligands (TTP, GLC, FRU), 14 pockets (best druggability 0.72). MolNFT v1 #111074 on GenesisL1: 3D structure, binding sites and…
- 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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