Research workbench
Crystal structure of human flap endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+
Analyse Crystal structure of human flap endonuclease FEN1 (D181A) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q8M
- Type
- protein + DNA
- Length
- 743 residues
- Chains
- 8
- 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
- K
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flap endonuclease 1 (EC 3.1.-.-) | protein | 335 | 53% helix, 10% strand | P39748 |
| B | Flap endonuclease 1 (EC 3.1.-.-) | protein | 334 | 54% helix, 11% strand | P39748 |
| D, G | 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, H | DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3') | dna | 12 | — | — |
| F, I | DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, G, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.84 | 0.86 | 97 | empty |
| 2 | 631 | 0.82 | 0.86 | 66 | empty |
| 3 | 213 | 0.63 | 0.83 | 36 | K |
| 4 | 199 | 0.61 | 0.82 | 37 | K |
| 5 | 103 | 0.44 | 0.79 | 13 | empty |
Interfaces
11 interfaces between chains.
- A–G · 917 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 861 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 605 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 537 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–E · 529 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Compared structures
- 3Q8M · Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate… · the same entry in another collection · chain I against I, TM-score 1.00
- P39748 · AlphaFold monomer V2.0 prediction for flap endonuclease 1 (P39748) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3Q8M · PDBe 3Q8M · UniProt P39748
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