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Flavobacterium johnsoniae GH31 dextranase, FJDEX31A, mutant D412A complexed with isomaltotriose

Analyse Flavobacterium johnsoniae GH31 dextranase, FJDEX31A, mutant D412A complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JR8
Type: protein
Length: 3,248 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Candidate alpha-glycosidase glycoside hydrolase family 31
EC: 3.2.1.20
UniProt: A5FBI1
Ligands: GLC
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Candidate alpha-glycosidase glycoside hydrolase family 31 (EC 3.2.1.20)	protein	812	22% helix, 30% strand	A5FBI1

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, B, C, D
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.76	0.79	97	MPD
2	803	0.76	0.80	72	MPD
3	703	0.73	0.79	59	MPD
4	390	0.66	0.79	46	GLC, ACT, MPD
5	333	0.65	0.80	46	GLC, ACT, MPD

Interfaces

4 interfaces between chains.

B–C · 929 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 918 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 908 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6JR8 · Flavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A complexed with… · 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 A5FBI1
Elsewhere: RCSB PDB 6JR8 · PDBe 6JR8 · UniProt A5FBI1

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