Research workbench
Structural basis for recognition of artificial DNA by an evolved klentaq variant
Analyse Structural basis for recognition of artificial DNA by an evolved klentaq variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W6Q
- Type
- protein + DNA
- Length
- 1,638 residues
- Chains
- 9
- 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*(1W5))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 515 | 52% helix, 14% strand | P19821 |
| B, E, H | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(1W5))-3') | dna | 12 | — | — |
| D, F, I | DNA (5'-D(P*GP*(1WA)P*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 13 | — | — |
| C | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 521 | 52% helix, 13% strand | P19821 |
| G | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 527 | 52% helix, 13% strand | P19821 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.72 | 0.88 | 26 | empty |
| 2 | 860 | 0.72 | 0.77 | 60 | empty |
| 3 | 227 | 0.71 | 0.87 | 25 | empty |
| 4 | 219 | 0.70 | 0.87 | 27 | empty |
| 5 | 265 | 0.60 | 0.80 | 35 | empty |
Interfaces
11 interfaces between chains.
- C–F · 1023 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 1001 Ų buried · 17 hydrogen bonds · protein-nucleic
- G–I · 989 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 825 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–E · 821 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 5W6Q · Structural basis for recognition of artificial DNA by an evolved KlenTaq variant · the same entry in another collection · chain I against I, 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 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 P19821
- Elsewhere: RCSB PDB 5W6Q · PDBe 5W6Q · UniProt P19821
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