MolNFT v1 · #12819 · protein + DNA
DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex
1KSP · DNA (5'-D(P*TP*TP*PST)-3'): “DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.55). MolNFT v1 #12819 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1KSP
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*PST)-3'); Protein (DNA polymerase I-klenow fragment (E.C.2.7.7.7))
- EC
- 2.7.7.7
- UniProt
- P00582
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(P*TP*TP*PST)-3') | dna | 3 | — | — |
| A | Protein (DNA polymerase I-klenow fragment (E.C.2.7.7.7)) (EC 2.7.7.7) | protein | 601 | 54% helix, 13% strand | P00582 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.55 | 0.81 | 23 | empty |
| 2 | 313 | 0.51 | 0.73 | 38 | ZN |
| 3 | 97 | 0.39 | 0.76 | 17 | empty |
| 4 | 89 | 0.37 | 0.75 | 16 | empty |
| 5 | 103 | 0.35 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 620 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 1KSP · PDBe 1KSP · UniProt P00582
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