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Structure of 3' phosphatase nexo (wt) from neisseria bound to DNA substrate

Analyse Structure of 3' phosphatase nexo (wt) 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: 6FK4
Type: protein + DNA
Length: 272 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease III; DNA (5'-D(P*GP*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)- 3')
EC: 3.1.11.2
UniProt: Q9K100
Pockets: 2 · best druggability 0.58

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease III (EC 3.1.11.2)	protein	257	29% helix, 26% strand	Q9K100
B	DNA (5'-D(PGPCPTPAPGPCPGPAPAPGPCPTPAPGP*A)- 3')	dna	15	—	—

Ligands and binding sites

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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.58	0.82	26	empty
2	75	0.36	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 798 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

6FK4 · Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9K100
Elsewhere: RCSB PDB 6FK4 · PDBe 6FK4 · UniProt Q9K100

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