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Bacteriophage lambda excisionase (xis)-DNA complex

Analyse Bacteriophage lambda excisionase (xis)-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1RH6
Type
protein + DNA
Length
135 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'…
UniProt
P03699
Pockets
3 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'dna14——
D5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3'dna14——
AExcisionaseprotein5527% helix, 25% strandP03699
BExcisionaseprotein5231% helix, 29% strandP03699

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13790.680.8225empty
21780.440.7524empty
3520.230.7212empty

Interfaces

6 interfaces between chains.

  • C–D · 620 Ų buried · 50 hydrogen bonds · nucleic-nucleic
  • D–B · 464 Ų buried · 12 hydrogen bonds · protein-nucleic
  • C–B · 446 Ų buried · 7 hydrogen bonds · protein-nucleic
  • A–B · 237 Ų buried · 3 hydrogen bonds · protein-protein
  • D–A · 135 Ų buried · 1 hydrogen bond · protein-nucleic

Compared structures

  • 1RH6 · Bacteriophage Lambda Excisionase (Xis)-DNA Complex · the same entry in another collection · chain C against C, TM-score 1.00

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