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MolNFT v1 · #13137 · protein + DNA

Mutm (fpg) DNA end-product structure

1L2B · 5'- D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Mutm (fpg) DNA end-product structure”. X-ray diffraction, 2 ligands (AD2, ZN), 1 pocket (best druggability 0.71). MolNFT v1 #13137 on GenesisL1: 3D structure, binding sites…

PDB
1L2B
Type
protein + DNA
Length
286 residues
Chains
4
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'…
Ligands
AD2, ZN
Pockets
1 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 25% 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*C*(AD2))-3'dna4——
D5'-D(P*GP*TP*CP*TP*AP*CP*C)-3'dna6——
AMutmprotein26430% helix, 25% strand—

Ligands and binding sites

  • AD2 · 2'-deoxy-adenosine-3'-5'-diphosphate · ligand · chains B, C, A
  • ZN · Zinc ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19120.710.7669AD2

Interfaces

4 interfaces between chains.

  • B–A · 440 Ų buried · 8 hydrogen bonds · protein-nucleic
  • D–A · 379 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–D · 258 Ų buried · 15 hydrogen bonds · nucleic-nucleic
  • B–C · 187 Ų buried · 10 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 1L2B · MutM (Fpg) DNA End-Product Structure · the same entry in another collection · chain B against B, TM-score 1.00

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