MolNFT v1 · #105885 · protein + DNA

FAN1 nuclease bound to 5' hydroxyl (dt-dt) single flap DNA

4RIC · Fanconi-associated nuclease 1: “FAN1 nuclease bound to 5' hydroxyl (dt-dt) single flap DNA”. X-ray diffraction, 1 ligand (CA), 16 pockets (best druggability 0.83). MolNFT v1 #105885 on GenesisL1: 3D structure, binding sites and…

PDB: 4RIC
Type: protein + DNA
Length: 1,321 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fanconi-associated nuclease 1; DNA (5'- D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP…
EC: 3.1.21.-, 3.1.4.1
UniProt: Q9Y2M0
Ligands: CA
Pockets: 16 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1)	protein	615	58% helix, 8% strand	Q9Y2M0
B	Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1)	protein	628	56% helix, 8% strand	Q9Y2M0
X, U	DNA (5'- D(TPTPAPGPCPCPAPCPGPCPCPTPAPGPAPCPTPCPCPTP*C)- 3')	dna	20	—	—
Y, V	DNA (5'-D(GPCPTPGPAPGPGPAPGPTPCPT)-3')	dna	12	—	—
W, T	DNA (5'-D(TPTPTPTPTPTPGPAPGPGPCPGPTPG)-3')	dna	7	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, U, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1024	0.83	0.85	54	empty
2	578	0.79	0.86	58	empty
3	216	0.71	0.87	46	empty
4	553	0.70	0.79	51	empty
5	582	0.68	0.78	31	empty

Interfaces

16 interfaces between chains.

A–U · 764 Å² buried · 14 hydrogen bonds · protein-nucleic
X–Y · 411 Å² buried · 48 hydrogen bonds · nucleic-nucleic
U–V · 405 Å² buried · 42 hydrogen bonds · nucleic-nucleic
A–T · 404 Å² buried · 13 hydrogen bonds · protein-nucleic
X–W · 347 Å² buried · 35 hydrogen bonds · nucleic-nucleic

Compared structures

4RIC · FAN1 Nuclease bound to 5' hydroxyl (dT-dT) single flap DNA · the same entry in another collection · chain T against T, TM-score 1.00
Q9Y2M0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 (Q9Y2M0) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9Y2M0
Elsewhere: RCSB PDB 4RIC · PDBe 4RIC · UniProt Q9Y2M0

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