MolNFT v1 · #41061 · protein

3'-5' exonuclease (nexo) from neisseria meningitidis

2JC4 · Exodeoxyribonuclease III: “3'-5' exonuclease (nexo) from neisseria meningitidis”. X-ray diffraction, 3 ligands (NA, MG, 2HP), 2 pockets (best druggability 0.39). MolNFT v1 #41061 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2JC4
Type: protein
Length: 256 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease III
EC: 3.1.11.2
UniProt: Q9K100
Ligands: NA, MG, 2HP
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease III (EC 3.1.11.2)	protein	256	30% helix, 26% strand	Q9K100

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · chains A
2HP · Dihydrogenphosphate ion · ion · chains A
1PE · Pentaethylene glycol · additive · chains A
ACT · Acetate ion · 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	69	0.39	0.79	16	empty
2	123	0.38	0.74	25	MG, ACT, 2HP

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2JC4 · 3'-5' exonuclease (NExo) from Neisseria Meningitidis · 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 2JC4 · PDBe 2JC4 · UniProt Q9K100

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