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Crystal structure of R192F HFEN1 in complex with DNA

Analyse Crystal structure of R192F HFEN1 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZOG
Type: protein + DNA
Length: 355 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flap endonuclease 1; DNA (5'-D(*CP*CP*CP*GP*TP*CP*C)-3'); DNA (5'…
EC: 3.1.-.-
UniProt: P39748
Pockets: 5 · best druggability 0.77

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	316	53% helix, 11% strand	P39748
B	DNA (5'-D(CPCPCPGPTPCP*C)-3')	dna	7	—	—
C	DNA (5'- D(PTPCPCPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGP*G)-3')	dna	19	—	—
D	DNA (5'-D(TPGPAPGPGPCPAPGPAPGPGPAP*T)-3')	dna	13	—	—

Pockets

5 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	1128	0.77	0.79	86	empty
2	120	0.51	0.81	21	empty
3	162	0.49	0.78	15	empty
4	111	0.38	0.75	19	empty
5	78	0.33	0.74	18	empty

Interfaces

5 interfaces between chains.

A–C · 704 Å² buried · 18 hydrogen bonds · protein-nucleic
C–D · 543 Å² buried · 53 hydrogen bonds · nucleic-nucleic
A–B · 374 Å² buried · 9 hydrogen bonds · protein-nucleic
B–C · 279 Å² buried · 26 hydrogen bonds · nucleic-nucleic
A–D · 272 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

5ZOG · Crystal Structure of R192F 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 0.96

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 5ZOG · PDBe 5ZOG · UniProt P39748

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