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Ternary complex structure of klenow fragment of taq DNA polymerase I707L mutant (CS3C klentaq) with DNA and ddctp
Analyse Ternary complex structure of klenow fragment of taq DNA polymerase I707L mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N5S
- Type
- protein + DNA
- Length
- 567 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*(DOC))-3'…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- DCT, MN, MG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3' | dna | 12 | — | — |
| C | 5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' | dna | 13 | — | — |
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 542 | 53% helix, 13% strand | P19821 |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains B, C, A
- MN · Manganese (II) ion · metal · 6 copies · chains B, A
- MG · Magnesium ion · metal · chains B, A
- ACT · Acetate ion · additive · 2 copies · chains B, C, A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C, A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.73 | 0.77 | 73 | MN, DCT |
| 2 | 209 | 0.69 | 0.87 | 27 | ACT |
| 3 | 270 | 0.62 | 0.80 | 34 | MN, EPE, ACT |
| 4 | 91 | 0.47 | 0.80 | 14 | empty |
| 5 | 97 | 0.36 | 0.74 | 15 | GOL |
Interfaces
3 interfaces between chains.
- C–A · 1014 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–A · 850 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 560 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4N5S · Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C… · 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 4N5S · PDBe 4N5S · UniProt P19821
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