MolNFT v1 · #141950 · protein + DNA

Crystal structure of D181A HFEN1 in complex with DNA

5ZOE · Flap endonuclease 1: “Crystal structure of D181A HFEN1 in complex with DNA”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.75). MolNFT v1 #141950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZOE
Type: protein + DNA
Length: 330 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flap endonuclease 1; DNA (5'- D(*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')…
EC: 3.1.-.-
UniProt: P39748
Ligands: K
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Flap endonuclease 1 (EC 3.1.-.-)	protein	290	50% helix, 12% strand	P39748
B	DNA (5'- D(CPCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPG)-3')	dna	18	—	—
C	DNA (5'-D(GPCPCPCPGPTPCPC)-3')	dna	8	—	—
D	DNA (5'-D(APCPTPTPTPGPAPGPGPCPAPGPAPG)-3')	dna	14	—	—

Ligands and binding sites

K · Potassium ion · metal · chains A, B

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

Pockets

3 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	828	0.75	0.79	64	K
2	431	0.58	0.75	42	empty
3	54	0.36	0.79	19	empty

Interfaces

5 interfaces between chains.

A–B · 795 Å² buried · 17 hydrogen bonds · protein-nucleic
B–D · 553 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–C · 425 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 294 Å² buried · 25 hydrogen bonds · nucleic-nucleic
A–D · 245 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

5ZOE · Crystal Structure of D181A hFen1 in complex with DNA · 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 0.98

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 5ZOE · PDBe 5ZOE · UniProt P39748

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