MolNFT v1 · #115218 · protein

The crystal structure of endo-1,4-D-glucanase from vibrio fischeri ES114

5CD2: “The crystal structure of endo-1,4-D-glucanase from vibrio fischeri ES114”. X-ray diffraction, 2 ligands (NI, CL), 2 pockets (best druggability 0.46). MolNFT v1 #115218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CD2
Type: protein
Length: 345 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-D-glucanase
EC: 3.2.1.4
UniProt: Q5DZ44
Ligands: NI, CL
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endo-1,4-D-glucanase (EC 3.2.1.4)	protein	345	48% helix, 17% strand	Q5DZ44

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 3 copies · 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	171	0.46	0.75	21	GOL
2	64	0.45	0.82	16	empty

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

5CD2 · The crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114 · 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 Q5DZ44
Elsewhere: RCSB PDB 5CD2 · PDBe 5CD2 · UniProt Q5DZ44

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