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Crystal structure of GH78 family rhamnosidase of bacillus sp. GL1 at 1.9 a

Analyse Crystal structure of GH78 family rhamnosidase of bacillus sp. GL1 at 1.9 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OKX
Type: protein
Length: 1,908 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhamnosidase B
EC: 3.2.1.40
UniProt: Q93RE7
Ligands: CA
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Rhamnosidase B (EC 3.2.1.40)	protein	954	24% helix, 32% strand	Q93RE7

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 43 copies · chains A, B

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

Pockets

18 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	1184	0.83	0.84	126	CA, GOL
2	352	0.82	0.92	42	empty
3	312	0.79	0.91	38	empty
4	248	0.74	0.88	45	GOL
5	565	0.71	0.79	56	GOL

Interfaces

1 interface between chains.

A–B · 2377 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

2OKX · Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A · 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 Q93RE7
Elsewhere: RCSB PDB 2OKX · PDBe 2OKX · UniProt Q93RE7

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