Research workbench
Crystal structures of the klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate
Analyse Crystal structures of the klenow fragment of DNA polymerase I complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KFD
- Type
- protein
- Length
- 560 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I klenow fragment
- EC
- 2.7.7.7
- UniProt
- P00582
- Ligands
- CTP
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I klenow fragment (EC 2.7.7.7) | protein | 560 | 54% helix, 14% strand | P00582 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.66 | 0.77 | 54 | empty |
| 2 | 241 | 0.47 | 0.74 | 29 | CTP |
| 3 | 90 | 0.36 | 0.75 | 16 | empty |
| 4 | 94 | 0.34 | 0.74 | 14 | empty |
Compared structures
- 1KFD · Crystal structures of the klenow fragment of DNA polymerase I complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00582 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P00582) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00582
- Elsewhere: RCSB PDB 1KFD · PDBe 1KFD · UniProt P00582
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