MolNFT v1 · #34325 · protein

A two-domain structure of alkaliphilic xynj from bacillus sp. 41M-1

2DCJ · Xylanase J: “A two-domain structure of alkaliphilic xynj from bacillus sp. 41M-1”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.68). MolNFT v1 #34325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DCJ
Type: protein
Length: 651 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylanase J
EC: 3.2.1.8
Ligands: CA
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylanase J (EC 3.2.1.8)	protein	327	5% helix, 60% strand	—
B	Xylanase J (EC 3.2.1.8)	protein	324	5% helix, 61% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 12 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	296	0.68	0.83	55	MPD, GOL
2	450	0.66	0.79	63	MPD
3	623	0.63	0.74	64	MPD, GOL
4	450	0.58	0.74	45	MPD
5	73	0.41	0.80	21	GOL

Interfaces

1 interface between chains.

A–B · 1526 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

2DCJ · A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1 · 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
Elsewhere: RCSB PDB 2DCJ · PDBe 2DCJ

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