MolNFT v1 · #119951 · protein

Structure of endoms in apo form

5GKJ · Endonuclease endoms: “Structure of endoms in apo form”. X-ray diffraction, 4 pockets (best druggability 0.48). MolNFT v1 #119951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GKJ
Type: protein
Length: 442 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease endoms
EC: 3.1.-.-
UniProt: Q5JER9
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endonuclease endoms (EC 3.1.-.-)	protein	213	23% helix, 43% strand	Q5JER9
B	Endonuclease endoms (EC 3.1.-.-)	protein	229	24% helix, 41% strand	Q5JER9

Pockets

4 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	208	0.48	0.75	28	empty
2	104	0.43	0.78	19	empty
3	59	0.31	0.76	15	empty
4	53	0.28	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 2360 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

5GKJ · Structure of EndoMS in apo form · the same entry in another collection · chain A against A, TM-score 1.00
Q5JER9 · AlphaFold monomer V2.0 prediction for endonuclease nucs (Q5JER9) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 Q5JER9
Elsewhere: RCSB PDB 5GKJ · PDBe 5GKJ · UniProt Q5JER9

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