Research workbench
Crystal structure of an active ternary complex of the large fragment of DNA polymerase I from thermus aquaticus
Analyse Crystal structure of an active ternary complex of the large fragment of DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KTQ
- Type
- protein + DNA
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)- 3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DCT, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)- 3') | dna | 12 | — | — |
| C | DNA (5'- D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 14 | — | — |
| A | Protein (large fragment of DNA polymerase I) (EC 2.7.7.7) | protein | 539 | 55% helix, 14% strand | P19821 |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.72 | 0.76 | 66 | MG, DCT |
| 2 | 220 | 0.68 | 0.86 | 27 | empty |
| 3 | 261 | 0.59 | 0.79 | 30 | empty |
| 4 | 76 | 0.42 | 0.80 | 17 | empty |
| 5 | 143 | 0.40 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1113 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–A · 837 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 560 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3KTQ · Crystal structure of an active ternary complex of the large fragment of DNA polymerase I… · 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 3KTQ · PDBe 3KTQ · UniProt P19821
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