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Crystal structure of pi initiator protein in complex with iteron DNA

Analyse Crystal structure of pi initiator protein in complex with iteron DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2NRA
Type
protein + DNA
Length
298 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP *CP*GP*TP*CP*T)-3'…
UniProt
P03067
Pockets
7 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP *CP*GP*TP*CP*T)-3'dna23——
B5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP *GP*TP*TP*CP*T)-3'dna23——
CPi proteinprotein25242% helix, 23% strandP03067

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12200.510.7629empty
2680.390.7916empty
31060.350.7419empty
4820.340.7521empty
5660.340.7712empty

Interfaces

3 interfaces between chains.

  • A–B · 988 Ų buried · 94 hydrogen bonds · nucleic-nucleic
  • B–C · 765 Ų buried · 22 hydrogen bonds · protein-nucleic
  • A–C · 734 Ų buried · 12 hydrogen bonds · protein-nucleic

Compared structures

  • 2NRA · Crystal structure of Pi initiator protein in complex with iteron DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P03067 · AlphaFold monomer V2.0 prediction for pi protein (P03067) · a predicted model of the same protein · chain C against A, TM-score 0.96

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