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Crystal structure of DFG5 from chaetomium thermophilum in complex with laminaribiose

Analyse Crystal structure of DFG5 from chaetomium thermophilum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RY7
Type: protein
Length: 410 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannan endo-1,6-alpha-mannosidase
EC: 3.2.1.101
UniProt: G0S3F2
Ligands: BGC, CA
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mannan endo-1,6-alpha-mannosidase (EC 3.2.1.101)	protein	410	55% helix, 4% strand	G0S3F2

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
CA · Calcium ion · metal · chains A
PGE · Triethylene glycol · additive · chains A

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

Pockets

3 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	94	0.46	0.80	26	empty
2	136	0.46	0.77	24	BGC
3	51	0.42	0.83	15	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6RY7 · Crystal structure of Dfg5 from Chaetomium thermophilum in complex with laminaribiose · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt G0S3F2
Elsewhere: RCSB PDB 6RY7 · PDBe 6RY7 · UniProt G0S3F2

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