MolNFT v1 · #136221 · protein + DNA

Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and SM3+

5UM9: “Flap endonuclease 1 (FEN1) D86N with 5'-flap substrate DNA and SM3+”. X-ray diffraction, 2 ligands (SM, K), 4 pockets (best druggability 0.78). MolNFT v1 #136221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UM9
Type: protein + DNA
Length: 380 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: 4 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Flap endonuclease 1 (EC 3.1.-.-)	protein	341	51% helix, 11% strand	P39748
D	DNA (5'- D(APCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPT)-3')	dna	18	—	—
E	DNA (5'-D(PTPCPTPTPGPAPGPGPCPAPGPAPGPT)-3')	dna	14	—	—
F	DNA (5'-D(APCPCPGPTPCP*C)-3')	dna	7	—	—

Ligands and binding sites

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

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	967	0.78	0.80	70	K
2	351	0.70	0.83	38	empty
3	91	0.44	0.80	13	empty
4	59	0.30	0.75	11	empty

Interfaces

5 interfaces between chains.

A–D · 1064 Å² buried · 12 hydrogen bonds · protein-nucleic
A–E · 914 Å² buried · 18 hydrogen bonds · protein-nucleic
D–E · 558 Å² buried · 43 hydrogen bonds · nucleic-nucleic
A–F · 396 Å² buried · 7 hydrogen bonds · protein-nucleic
D–F · 269 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

5UM9 · Flap endonuclease 1 (FEN1) D86N 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 5UM9 · PDBe 5UM9 · UniProt P39748

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.