MolNFT v1 · #6206 · protein

Crystal structure of xynb, a highly thermostable beta-1,4- xylanase from dictyoglomus thermophilum RT46B.1, at 1.8 a resolution

1F5J · Beta-1,4-xylanase: “Crystal structure of xynb, a highly thermostable beta-1,4- xylanase from dictyoglomus thermophilum RT46B.1…”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.61). MolNFT v1 #6206 on GenesisL1…

PDB: 1F5J
Type: protein
Length: 398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-1,4-xylanase
EC: 3.2.1.8
UniProt: P77853
Ligands: SO4
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-1,4-xylanase (EC 3.2.1.8)	protein	199	8% helix, 65% strand	P77853

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B

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	247	0.61	0.81	39	empty
2	138	0.51	0.80	29	empty
3	137	0.49	0.79	26	empty

Interfaces

1 interface between chains.

A–B · 515 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1F5J · Crystal structure of xynb, a highly thermostable beta-1,4-xylanase from dictyoglomus… · 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 P77853
Elsewhere: RCSB PDB 1F5J · PDBe 1F5J · UniProt P77853

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