Research workbench

Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and SM3+

Analyse Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and SM3+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KSE
Type: protein + DNA
Length: 381 residues
Chains: 4
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: 7 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Flap endonuclease 1 (EC 3.1.-.-)	protein	341	53% helix, 11% strand	P39748
D	DNA (5'- D(APCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPT)-3')	dna	18	—	—
E	DNA (5'-D(PTPAPAPTPTPGPAPGPGPCPAPGPAPGP*T)- 3')	dna	15	—	—
F	DNA (5'-D(APCPCPGPTPCP*C)-3')	dna	7	—	—

Ligands and binding sites

SM · Samarium (III) ion · metal · 5 copies · chains A, E
K · Potassium ion · metal · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	440	0.73	0.83	46	empty
2	1197	0.72	0.76	74	K
3	219	0.61	0.82	27	SM
4	118	0.42	0.77	12	empty
5	98	0.42	0.78	15	empty

Interfaces

5 interfaces between chains.

A–D · 951 Å² buried · 16 hydrogen bonds · protein-nucleic
A–E · 788 Å² buried · 12 hydrogen bonds · protein-nucleic
D–E · 525 Å² buried · 50 hydrogen bonds · nucleic-nucleic
A–F · 390 Å² buried · 6 hydrogen bonds · protein-nucleic
D–F · 272 Å² buried · 24 hydrogen bonds · nucleic-nucleic

Compared structures

5KSE · Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA 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 5KSE · PDBe 5KSE · UniProt P39748

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