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I-CREI(Q47E)/DNA complex

Analyse I-CREI(Q47E)/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1T9J
Type
protein + DNA
Length
350 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*TP*CP*G)-3'…
EC
3.1.-.-
UniProt
P05725
Pockets
4 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 21% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*TP*CP*G)-3'dna24——
D5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *TP*TP*TP*TP*GP*C)-3'dna24——
A, BDNA endonuclease I-crei (EC 3.1.-.-)protein15157% helix, 21% strandP05725

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1850.720.9524empty
2920.670.9225empty
3530.430.8421empty
4600.430.8319empty

Interfaces

6 interfaces between chains.

  • C–D · 1173 Ų buried · 97 hydrogen bonds · nucleic-nucleic
  • A–B · 983 Ų buried · 13 hydrogen bonds · protein-protein
  • C–A · 975 Ų buried · 26 hydrogen bonds · protein-nucleic
  • D–B · 966 Ų buried · 23 hydrogen bonds · protein-nucleic
  • C–B · 882 Ų buried · 15 hydrogen bonds · protein-nucleic

Compared structures

  • 1T9J · I-CreI(Q47E)/DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
  • P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

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