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Crystal structure of PAFAN1 - 5' flap DNA complex

Analyse Crystal structure of PAFAN1 - 5' flap DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R8A
Type: protein + DNA
Length: 1,168 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein; DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)- 3')…
UniProt: Q9I2N0
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Uncharacterized protein	protein	538	51% helix, 8% strand	Q9I2N0
B, G	DNA (5'-D(PAPCPCPAPGPAPCPAPCPAPCPAPTPTP*C)- 3')	dna	15	—	—
C, H	DNA (5'-D(PGPTPTPGPGPGPAPTPTPG)-3')	dna	10	—	—
D, I	DNA (5'- D(PGPAPAPTPGPTPGPTPGPTPCPTPCPAPAPTPCPCPCPAP*A)- 3')	dna	21	—	—

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.79	0.81	77	empty
2	571	0.76	0.83	44	empty
3	326	0.71	0.84	47	empty
4	352	0.65	0.80	30	empty
5	477	0.63	0.77	32	empty

Interfaces

10 interfaces between chains.

F–G · 1100 Å² buried · 27 hydrogen bonds · protein-nucleic
A–B · 1093 Å² buried · 26 hydrogen bonds · protein-nucleic
A–D · 758 Å² buried · 20 hydrogen bonds · protein-nucleic
F–I · 755 Å² buried · 21 hydrogen bonds · protein-nucleic
B–D · 524 Å² buried · 39 hydrogen bonds · nucleic-nucleic

Compared structures

4R8A · Crystal structure of paFAN1 - 5' flap DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
Q9I2N0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 homolog (Q9I2N0) · a predicted model of the same protein · chain F 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 Q9I2N0
Elsewhere: RCSB PDB 4R8A · PDBe 4R8A · UniProt Q9I2N0

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