MolNFT v1 · #138039 · protein + DNA
Structural basis for recognition of artificial DNA by an evolved klentaq variant
5W6Q · DNA polymerase I, thermostable: “Structural basis for recognition of artificial DNA by an evolved klentaq variant”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #138039 on GenesisL1: 3D structure, binding sites…
- 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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