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MolNFT v1 · #21038 · protein + DNA

Crystal structure of a. fulgidus fen-1 bound to DNA

1RXW · 5'-D(*C*PG*PA*PT*PG*PC*PT*PA)-3': “Crystal structure of a. fulgidus fen-1 bound to DNA”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #21038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1RXW
Type
protein + DNA
Length
320 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*C*PG*PA*PT*PG*PC*PT*PA)-3'; 5'-D(*T*PA*PG*PC*PA*PT*PC*PG*PG)-3'; Flap…
UniProt
O29975
Pockets
5 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 11% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*C*PG*PA*PT*PG*PC*PT*PA)-3'dna7——
C5'-D(*T*PA*PG*PC*PA*PT*PC*PG*PG)-3'dna8——
AFlap structure-specific endonucleaseprotein30554% helix, 11% strandO29975

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14250.620.7743empty
2840.570.8723empty
3920.410.7718empty
4600.340.7714empty
5600.290.7412empty

Interfaces

3 interfaces between chains.

  • B–A · 445 Ų buried · 8 hydrogen bonds · protein-nucleic
  • C–A · 396 Ų buried · 7 hydrogen bonds · protein-nucleic
  • B–C · 329 Ų buried · 32 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1RXW · Crystal structure of A. fulgidus FEN-1 bound to DNA · the same entry in another collection · chain B against B, TM-score 1.00
  • O29975 · AlphaFold monomer V2.0 prediction for flap endonuclease 1 (O29975) · a predicted model of the same protein · chain A against A, TM-score 0.98

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