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Structure of no-DNA complex

Analyse Structure of no-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4GCK
Type
protein + DNA
Length
782 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Nucleoid occlusion factor slma; DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
UniProt
B5XTG2
Pockets
15 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, CNucleoid occlusion factor slmaprotein19078% helix, 0% strandB5XTG2
B, DNucleoid occlusion factor slmaprotein18976% helix, 0% strandB5XTG2
W, ZDNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')dna12——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14030.570.7537empty
24000.570.7536empty
3680.540.8721empty
4990.520.8318empty
5750.500.8418empty

Interfaces

11 interfaces between chains.

  • A–B · 1692 Ų buried · 35 hydrogen bonds · protein-protein
  • C–D · 1677 Ų buried · 33 hydrogen bonds · protein-protein
  • W–Z · 523 Ų buried · 43 hydrogen bonds · nucleic-nucleic
  • A–Z · 336 Ų buried · 9 hydrogen bonds · protein-nucleic
  • C–W · 335 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 4GCK · structure of no-dna complex · the same entry in another collection · chain Z against Z, TM-score 1.00
  • B5XTG2 · AlphaFold monomer V2.0 prediction for nucleoid occlusion factor slma (B5XTG2) · a predicted model of the same protein · chain A against A, TM-score 0.99

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