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Crystal structure of bacillus subtilis family-11 xylanase

Analyse Crystal structure of bacillus subtilis family-11 xylanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DCY
Type: protein
Length: 925 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase a
EC: 3.2.1.8
UniProt: P18429
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Endo-1,4-beta-xylanase a (EC 3.2.1.8)	protein	185	5% helix, 64% strand	P18429

Ligands and binding sites

TLA · L(+)-tartaric acid · additive · 6 copies · chains A, B, C, E
DIO · 1,4-diethylene dioxide · additive · 3 copies · chains A, B, C
TAR · D(-)-tartaric acid · additive · chains A, E

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.82	0.83	143	TLA
2	425	0.69	0.81	55	TAR, TLA
3	112	0.51	0.81	26	DIO
4	108	0.43	0.77	25	empty
5	144	0.42	0.75	23	empty

Interfaces

5 interfaces between chains.

A–B · 864 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 490 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 455 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 417 Å² buried · 1 hydrogen bond · protein-protein
B–E · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2DCY · Crystal structure of Bacillus subtilis family-11 xylanase · the same entry in another collection · chain A against A, TM-score 1.00
P18429 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P18429) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P18429
Elsewhere: RCSB PDB 2DCY · PDBe 2DCY · UniProt P18429

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