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Mutm set 1 gpgo

Analyse Mutm set 1 gpgo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3U6D
Type
protein + DNA
Length
275 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Formamidopyrimidine-DNA glycosylase; DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*CP*GP*AP*CP*G…
EC
3.2.2.23
UniProt
P84131
Ligands
ZN
Pockets
3 · best druggability 0.66

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AFormamidopyrimidine-DNA glycosylase (EC 3.2.2.23)protein25231% helix, 26% strandP84131
BDNA (5'-D(*A*GP*GP*TP*AP*GP*AP*TP*CP*CP*CP*GP*AP*CP*GP*C)- 3')dna13——
CDNA (5'-D(*TP*GP*CP*GP*TP*CP*GP*(8OG)P*GP*AP*(TX) P*CP*TP*AP*CP*C)-3')dna10——

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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14790.660.7840empty
21170.440.7818empty
3910.340.7416empty

Interfaces

3 interfaces between chains.

  • A–C · 699 Ų buried · 12 hydrogen bonds · protein-nucleic
  • B–C · 471 Ų buried · 43 hydrogen bonds · nucleic-nucleic
  • A–B · 427 Ų buried · 11 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 3U6D · MutM set 1 GpGo · the same entry in another collection · chain A against A, TM-score 1.00

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