MolNFT v1 · #148906 · protein + DNA

Structure of 3' phosphatase nexo (D146N) from neisseria bound to product DNA hairpin

6FKE · Exodeoxyribonuclease III: “Structure of 3' phosphatase nexo (D146N) from neisseria bound to product DNA hairpin”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.50). MolNFT v1 #148906 on GenesisL1: 3D structure…

PDB: 6FKE
Type: protein + DNA
Length: 269 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease III; DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')
EC: 3.1.11.2
UniProt: Q9K100
Ligands: MN
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease III (EC 3.1.11.2)	protein	257	31% helix, 26% strand	Q9K100
B	DNA (5'-D(GPTPAPGPCPGPAPAPGPCPTPA)-3')	dna	12	—	—

Ligands and binding sites

MN · Manganese (II) 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	140	0.50	0.79	22	empty
2	70	0.33	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 745 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

6FKE · Structure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin · 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 6FKE · PDBe 6FKE · UniProt Q9K100

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