MolNFT v1 · #124236 · protein + DNA
Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and SM3+
5K97: “Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and SM3+”. X-ray diffraction, 2 ligands (SM, K), 6 pockets (best druggability 0.80). MolNFT v1 #124236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K97
- Type
- protein + DNA
- Length
- 379 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flap endonuclease 1; DNA (5'- D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')…
- EC
- 3.1.-.-
- UniProt
- P39748
- Ligands
- SM, K
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flap endonuclease 1 (EC 3.1.-.-) | protein | 341 | 52% helix, 10% strand | P39748 |
| D | DNA (5'- D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3') | dna | 18 | — | — |
| E | DNA (5'-D(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3') | dna | 7 | — | — |
| G | DNA (5'-D(P*TP*T)-3') | dna | 2 | — | — |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 8 copies · chains A, E
- K · Potassium ion · metal · chains A, D
- EDO · 1,2-ethanediol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.80 | 0.82 | 83 | EDO |
| 2 | 129 | 0.39 | 0.75 | 16 | empty |
| 3 | 76 | 0.39 | 0.79 | 14 | empty |
| 4 | 73 | 0.29 | 0.73 | 10 | empty |
| 5 | 61 | 0.28 | 0.74 | 8 | empty |
Interfaces
7 interfaces between chains.
- A–D · 905 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–E · 476 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–E · 447 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–G · 388 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–F · 375 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5K97 · Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+ · the same entry in another collection · chain A against A, TM-score 1.00
- P39748 · AlphaFold monomer V2.0 prediction for flap endonuclease 1 (P39748) · 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 P39748
- Elsewhere: RCSB PDB 5K97 · PDBe 5K97 · UniProt P39748
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