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Sequence-matched mutm interrogation complex 5 (IC5)

Analyse Sequence-matched mutm interrogation complex 5 (IC5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3GQ5
Type
protein + DNA
Length
274 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA glycosylase; DNA (5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)- 3'); DNA…
EC
4.2.99.18
UniProt
P84131
Ligands
ZN
Pockets
2 · best druggability 0.66

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA glycosylase (EC 4.2.99.18)protein25231% helix, 26% strandP84131
BDNA (5'-D(*A*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)- 3')dna12——
CDNA (5'-D(*TP*GP*CP*GP*T*CP*CP*GP*GP*GP*TP*CP*TP*AP*CP*C)- 3')dna10——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains A
  • GOL · Glycerol · additive · 2 copies · 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
14830.660.7837empty
21260.420.7621empty

Interfaces

3 interfaces between chains.

  • A–C · 656 Ų buried · 13 hydrogen bonds · protein-nucleic
  • B–C · 492 Ų buried · 47 hydrogen bonds · nucleic-nucleic
  • A–B · 470 Ų buried · 11 hydrogen bonds · protein-nucleic

Compared structures

  • 3GQ5 · Sequence-matched MutM Interrogation Complex 5 (IC5) · the same entry in another collection · chain A against A, TM-score 1.00

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