MolNFT v2 · #225339 · protein

The crystal structure of a GH3 enzyme CcBgl3B with glycerol

8XRU: “The crystal structure of a GH3 enzyme CcBgl3B with glycerol”. X-ray diffraction at 2.02, 1 ligand (CA), 20 pockets (best druggability 0.85). MolNFT v2 #225339 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8XRU
Type: protein
Length: 1,682 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.02
Source: Cellulosimicrobium
Molecule: GH3 enzyme CcBgl3B
Ligands: CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · resolution 2.02 · 3 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GH3 enzyme CcBgl3B	protein	751	33% helix, 21% strand	—
B	GH3 enzyme CcBgl3B	protein	747	33% helix, 21% strand	—
C	GH3 enzyme CcBgl3B	protein	184	21% helix, 20% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.85	0.96	36	empty
2	56	0.61	0.92	15	empty
3	333	0.60	0.78	30	empty
4	296	0.59	0.78	25	empty
5	362	0.59	0.76	58	empty

Interfaces

2 interfaces between chains.

A–B · 2803 Å² buried · 51 hydrogen bonds · protein-protein
B–C · 408 Å² buried · 7 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8XRU · PDBe 8XRU

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