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Structure of the C. elegans nucleoside hydrolase

Analyse Structure of the C. elegans nucleoside hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MJ7
Type: protein
Length: 643 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: Q9XWN7
Ligands: CA
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein	protein	322	41% helix, 17% strand	Q9XWN7
B	Uncharacterized protein	protein	321	41% helix, 16% strand	Q9XWN7

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	383	0.69	0.81	40	CA, TRS
2	368	0.67	0.80	36	CA, TRS
3	54	0.37	0.80	15	empty
4	104	0.37	0.74	22	empty
5	63	0.31	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 926 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5MJ7 · Structure of the C. elegans nucleoside hydrolase · 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 Q9XWN7
Elsewhere: RCSB PDB 5MJ7 · PDBe 5MJ7 · UniProt Q9XWN7

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