MolNFT v1 · #86674 · protein + DNA
Crystal structure of bacillus DNA polymerase I fragment complexed to 11 base pairs of duplex DNA after addition of two datp residues
4BDP · DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3'): “Crystal structure of bacillus DNA polymerase I fragment complexed to 11 base pairs of duplex DNA after…”. X-ray diffraction, 2 ligands (MG, SO4), 8 pockets (best druggability 0.72).…
- PDB
- 4BDP
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3'); DNA (5'…
- UniProt
- P52026
- Ligands
- MG, SO4
- Pockets
- 8 · 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*AP*TP*CP*AP*TP*GP*CP*AP*A)-3') | dna | 11 | — | — |
| T | DNA (5'- D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3') | dna | 13 | — | — |
| A | Protein (DNA polymerase I) | protein | 580 | 56% helix, 13% strand | P52026 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.72 | 0.86 | 30 | empty |
| 2 | 390 | 0.70 | 0.82 | 42 | empty |
| 3 | 625 | 0.65 | 0.75 | 56 | SO4, MG |
| 4 | 126 | 0.46 | 0.78 | 26 | empty |
| 5 | 152 | 0.43 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1203 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–A · 920 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–T · 503 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 4BDP · Crystal structure of bacillus DNA polymerase I fragment complexed to 11 base pairs of… · the same entry in another collection · chain P against P, TM-score 1.00
- P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P52026
- Elsewhere: RCSB PDB 4BDP · PDBe 4BDP · UniProt P52026
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