GL1X · GenesisL1 explorer

MolNFT v1 · #78497 · protein + DNA

Mutm slanted complex 1

3SAR · Formamidopyrimidine-DNA glycosylase: “Mutm slanted complex 1”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.60). MolNFT v1 #78497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3SAR
Type
protein + DNA
Length
280 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Formamidopyrimidine-DNA glycosylase; 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)…
EC
3.2.2.23
UniProt
P84131
Ligands
ZN
Pockets
2 · best druggability 0.60

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AFormamidopyrimidine-DNA glycosylase (EC 3.2.2.23)protein25331% helix, 26% strandP84131
C5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'dna14——
D5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*(CX2) P*TP*AP*CP*C)- 3'dna13——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A
  • GOL · Glycerol · additive · 4 copies · chains A, D

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13110.600.7946GOL
21720.530.8022empty

Interfaces

3 interfaces between chains.

  • A–D · 656 Ų buried · 8 hydrogen bonds · protein-nucleic
  • C–D · 635 Ų buried · 55 hydrogen bonds · nucleic-nucleic
  • A–C · 544 Ų buried · 13 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 3SAR · MUTM Slanted complex 1 · the same entry in another collection · chain A against A, TM-score 1.00

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