MolNFT v1 · #105745 · protein + DNA

A nuclease DNA complex

4REA · Fanconi-associated nuclease 1: “A nuclease DNA complex”. X-ray diffraction, 11 pockets (best druggability 0.76). MolNFT v1 #105745 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4REA
Type: protein + DNA
Length: 1,215 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fanconi-associated nuclease 1; DNA (5'-D(*TP*GP*CP*TP*CP*GP*CP*CP*AP*C)-3'); DNA…
EC: 3.1.21.-, 3.1.4.1
UniProt: Q9Y2M0
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1)	protein	590	59% helix, 7% strand	Q9Y2M0
B	Fanconi-associated nuclease 1 (EC 3.1.21.-, 3.1.4.1)	protein	588	60% helix, 6% strand	Q9Y2M0
C	DNA (5'-D(TPGPCPTPCPGPCPCPAPC)-3')	dna	10	—	—
D	DNA (5'-D(PCPGPTPGPGPCPGPAPGPC)-3')	dna	10	—	—
E	DNA (5'- D(PGPGPCPGPAPGPCPGPCPTPCPGPCPCPAPCP*G)-3')	dna	17	—	—

Pockets

11 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	806	0.76	0.80	83	empty
2	708	0.74	0.80	73	empty
3	945	0.74	0.77	81	empty
4	628	0.68	0.78	40	empty
5	451	0.63	0.76	31	empty

Interfaces

8 interfaces between chains.

A–B · 1107 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 539 Å² buried · 61 hydrogen bonds · nucleic-nucleic
B–C · 492 Å² buried · 11 hydrogen bonds · protein-nucleic
C–E · 203 Å² buried · 8 hydrogen bonds · nucleic-nucleic
A–D · 183 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

4REA · A Nuclease DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2M0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 (Q9Y2M0) · a predicted model of the same protein · chain B 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 Q9Y2M0
Elsewhere: RCSB PDB 4REA · PDBe 4REA · UniProt Q9Y2M0

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