GL1X · GenesisL1 explorer

MolNFT v1 · #36438 · protein + DNA

Mutm crosslinked to undamaged DNA sampling G:C base pair IC3

2F5O · 5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3': “Mutm crosslinked to undamaged DNA sampling G:C base pair IC3”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #36438 on GenesisL1: 3D…

PDB
2F5O
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*TP*CP*CP*GP*GP*AP*CP*GP*C)-3'…
EC
3.2.2.23
UniProt
P84131
Ligands
ZN
Pockets
3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*AP*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*GP*C)-3'dna14——
C5'-D(*TP*GP*C*GP*TP*CP*CP*GP*GP*AP*TP*CP*TP*AP*CP*C)-3'dna13——
AFormamidopyrimidine-DNA glycosidase (EC 3.2.2.23)protein25231% helix, 26% strandP84131

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A
  • GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15090.680.7943empty
21030.430.7917empty
31090.350.7421empty

Interfaces

3 interfaces between chains.

  • C–A · 598 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–C · 586 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • B–A · 428 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 2F5O · MutM crosslinked to undamaged DNA sampling G:C base pair IC3 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.