MolNFT v1 · #42331 · protein + DNA
Klenow fragment with bridging-sulfur substrate and manganese
2KFN · 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3': “Klenow fragment with bridging-sulfur substrate and manganese”. X-ray diffraction, 3 ligands (ZN, MN, MG), 7 pockets (best druggability 0.53). MolNFT v1 #42331 on GenesisL1: 3D structure, binding…
- PDB
- 2KFN
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3'; Klenow fragment of DNA polymerase I
- EC
- 2.7.7.7
- UniProt
- P00582
- Ligands
- ZN, MN, MG
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3' | dna | 3 | — | — |
| A | Klenow fragment of DNA polymerase I (EC 2.7.7.7) | protein | 601 | 51% helix, 13% strand | P00582 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B, A
- MN · Manganese (II) ion · metal · chains B, A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.53 | 0.80 | 21 | empty |
| 2 | 302 | 0.50 | 0.73 | 43 | ZN |
| 3 | 66 | 0.42 | 0.81 | 19 | empty |
| 4 | 100 | 0.38 | 0.76 | 18 | empty |
| 5 | 96 | 0.37 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 654 Ų buried · 17 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 2KFN · PDBe 2KFN · UniProt P00582
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