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MolNFT v1 · #36439 · protein + DNA

Mutm crosslinked to undamaged DNA sampling A:T base pair IC2

2F5P · 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3': “Mutm crosslinked to undamaged DNA sampling A:T base pair IC2”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.68). MolNFT v1 #36439 on GenesisL1: 3D…

PDB
2F5P
Type
protein + DNA
Length
279 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*TP*TP*GP*GP*AP*CP*GP*C)-3'…
EC
3.2.2.23
UniProt
P84131
Ligands
ZN
Pockets
2 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3'dna13——
D5'-D(*TP*GP*CP*G*TP*CP*CP*AP*AP*GP*TP*CP*TP*AP*CP*C)-3'dna12——
AFormamidopyrimidine-DNA glycosidase (EC 3.2.2.23)protein25430% helix, 26% 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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15360.680.7942empty
21470.460.7720empty

Interfaces

3 interfaces between chains.

  • D–A · 649 Ų buried · 12 hydrogen bonds · protein-nucleic
  • C–D · 550 Ų buried · 44 hydrogen bonds · nucleic-nucleic
  • C–A · 483 Ų buried · 12 hydrogen bonds · protein-nucleic

Compared structures

  • 2F5P · MutM crosslinked to undamaged DNA sampling A:T base pair IC2 · the same entry in another collection · chain C against C, TM-score 1.00

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