MolNFT v1 · #141216 · protein

Crystal structure of beta-1,2-glucanase from parabacteroides distasonis

5Z06 · BDI_3064 protein: “Crystal structure of beta-1,2-glucanase from parabacteroides distasonis”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.85). MolNFT v1 #141216 on GenesisL1: 3D structure, binding sites and…

PDB: 5Z06
Type: protein
Length: 1,395 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BDI_3064 protein
UniProt: A6LGF6
Ligands: CA
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BDI_3064 protein	protein	697	30% helix, 24% strand	A6LGF6
B	BDI_3064 protein	protein	698	31% helix, 24% strand	A6LGF6

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 10 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.85	0.88	91	empty
2	649	0.84	0.89	76	GOL
3	284	0.61	0.79	35	GOL
4	301	0.61	0.78	35	GOL
5	135	0.56	0.82	27	empty

Interfaces

1 interface between chains.

A–B · 992 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5Z06 · Crystal structure of beta-1,2-glucanase from Parabacteroides distasonis · 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 A6LGF6
Elsewhere: RCSB PDB 5Z06 · PDBe 5Z06 · UniProt A6LGF6

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