MolNFT v1 · #89550 · protein + DNA
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with duplex DNA, dgtp and calcium
4DSJ: “Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with duplex DNA, dgtp and…”. X-ray diffraction, 2 ligands (DGT, CA), 19 pockets (best druggability 0.72). MolNFT v1 #89550 on GenesisL1: 3D structure…
- PDB
- 4DSJ
- Type
- protein + DNA
- Length
- 1,198 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA; Dgtp
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- DGT, CA
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 579 | 56% helix, 13% strand | D9N168 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 575 | 49% helix, 13% strand | D9N168 |
| C, E | DNA | dna | 12 | — | — |
| D, F | Dgtp | dna | 10 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.72 | 0.76 | 67 | DGT, CA |
| 2 | 334 | 0.72 | 0.85 | 35 | empty |
| 3 | 655 | 0.69 | 0.77 | 61 | empty |
| 4 | 382 | 0.69 | 0.82 | 46 | empty |
| 5 | 339 | 0.64 | 0.80 | 40 | empty |
Interfaces
11 interfaces between chains.
- A–C · 923 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–F · 848 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 838 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 837 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 488 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DSJ · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with… · 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 D9N168
- Elsewhere: RCSB PDB 4DSJ · PDBe 4DSJ · UniProt D9N168
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