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MolNFT v1 · #148897 · protein + DNA

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

6FK5 · Nexo D146N: “Structure of 3' phosphatase nexo (D146N) from neisseria bound to DNA substrate in presence of magnesium ion”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.48). MolNFT v1 #148897 on GenesisL1: 3D…

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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