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Structure of 3' phosphatase nexo (D146N) from neisseria bound to DNA substrate in presence of magnesium ion

Analyse Structure of 3' phosphatase nexo (D146N) from neisseria bound to DNA substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6FK5
Type
protein + DNA
Length
270 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Nexo D146N; DNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')
UniProt
A0A0A8F5K9
Ligands
MG
Pockets
2 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ANexo D146Nprotein25729% helix, 26% strandA0A0A8F5K9
BDNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')dna13——

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains A, B
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11100.480.8020empty
2700.330.7517empty

Interfaces

1 interface between chains.

  • A–B · 704 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 6FK5 · Structure of 3' phosphatase NExo (D146N) from Neisseria bound to DNA substrate in… · the same entry in another collection · chain A against A, TM-score 1.00

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