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Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing DNA

Analyse Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1R2Z
Type
protein + DNA
Length
297 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'- D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'…
UniProt
P84131
Ligands
ZN
Pockets
3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'- D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'dna12——
C5'-D(*TP*GP*CP*GP*TP*CP*CP*AP*(DHU) P*GP*TP*CP*TP*AP*CP*C)-3'dna12——
AMutmprotein27330% helix, 24% strandP84131

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15420.670.7844empty
23270.570.7644empty
31050.420.7818empty

Interfaces

3 interfaces between chains.

  • C–A · 747 Ų buried · 20 hydrogen bonds · protein-nucleic
  • B–C · 484 Ų buried · 31 hydrogen bonds · nucleic-nucleic
  • B–A · 362 Ų buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 1R2Z · MutM (Fpg) bound to 5,6-dihydrouracil (DHU) containing DNA · the same entry in another collection · chain B against B, TM-score 1.00

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