MolNFT v1 · #19753 · protein + DNA
Ddttp-trapped closed ternary complex of the large fragment of DNA polymerase I from thermus aquaticus
1QTM · 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3': “Ddttp-trapped closed ternary complex of the large fragment of DNA polymerase I from thermus aquaticus”. X-ray diffraction, 2 ligands (TTP, MG), 8 pockets (best druggability 0.70).…
- PDB
- 1QTM
- Type
- protein + DNA
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- TTP, MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3' | dna | 12 | — | — |
| C | 5'-D(*AP*AP*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3' | dna | 14 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 539 | 54% helix, 14% strand | P19821 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains B, C, A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.70 | 0.82 | 39 | MG, TTP |
| 2 | 224 | 0.69 | 0.86 | 25 | empty |
| 3 | 790 | 0.66 | 0.74 | 51 | empty |
| 4 | 249 | 0.59 | 0.79 | 31 | empty |
| 5 | 81 | 0.48 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1100 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–A · 821 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 552 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1QTM · Ddttp-trapped closed ternary complex of the large fragment of DNA polymerase I from… · the same entry in another collection · chain B against B, 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 1QTM · PDBe 1QTM · UniProt P19821
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