MolNFT v1 · #117302 · protein + DNA
Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with 5-(N-(10- hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate
5E41 · DNA polymerase I, thermostable: “Crystal structure of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary…”. X-ray diffraction, 2 ligands (AUL, MG), 7 pockets (best druggability 0.81). MolNFT v1 #117302…
- PDB
- 5E41
- Type
- protein + DNA
- Length
- 568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- AUL, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 540 | 54% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- AUL · 2'-deoxy-5-{(1E)-5-[(10-hydroxydecanoyl)amino]pent-1-en-1-yl}uridine 5'-(tetrahydrogen triphosphate) · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.81 | 0.82 | 74 | MG, AUL |
| 2 | 204 | 0.70 | 0.88 | 24 | empty |
| 3 | 281 | 0.60 | 0.79 | 33 | empty |
| 4 | 105 | 0.52 | 0.82 | 19 | empty |
| 5 | 126 | 0.44 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1459 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 793 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 570 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5E41 · Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a… · the same entry in another collection · chain A against A, TM-score 1.00
- P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P19821
- Elsewhere: RCSB PDB 5E41 · PDBe 5E41 · UniProt P19821
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