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Complex structure of gh 113 family beta-1,4-mannanase with mannobiose

Analyse Complex structure of gh 113 family beta-1,4-mannanase with mannobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YLK
Type: protein
Length: 618 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-1,4-mannanase
UniProt: K0J0N5
Ligands: BMA
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Beta-1,4-mannanase	protein	309	39% helix, 20% strand	K0J0N5

Ligands and binding sites

BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.62	0.79	36	BMA
2	301	0.60	0.78	39	BMA
3	87	0.40	0.78	16	empty

Interfaces

1 interface between chains.

B–A · 1067 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5YLK · Complex structure of GH 113 family beta-1,4-mannanase with mannobiose · the same entry in another collection · chain B against B, 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 K0J0N5
Elsewhere: RCSB PDB 5YLK · PDBe 5YLK · UniProt K0J0N5

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