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MolNFT v1 · #13139 · protein + DNA

Mutm (fpg)-DNA estranged guanine mismatch recognition complex

1L2D · 5'- D(*AP*G*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3': “Mutm (fpg)-DNA estranged guanine mismatch recognition complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.69). MolNFT v1 #13139 on GenesisL1: 3D…

PDB
1L2D
Type
protein + DNA
Length
283 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'- D(*AP*G*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'…
Ligands
ZN
Pockets
2 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'- D(*AP*G*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'dna12——
C5'-D(*TP*GP*C*GP*TP*CP*CP*AP*(HPD) P*GP*TP*CP*TP*AP*CP*C)-3'dna12——
AMutmprotein25931% helix, 25% strand—

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
16530.690.7848empty
2640.280.7312empty

Interfaces

3 interfaces between chains.

  • C–A · 629 Ų buried · 16 hydrogen bonds · protein-nucleic
  • B–C · 472 Ų buried · 42 hydrogen bonds · nucleic-nucleic
  • B–A · 434 Ų buried · 6 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 1L2D · MutM (Fpg)-DNA Estranged Guanine Mismatch Recognition Complex · the same entry in another collection · chain B against B, TM-score 1.00

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