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Structure of GH10 from paenibacillus barcinonensis

Analyse Structure of GH10 from paenibacillus barcinonensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4W8L
Type: protein
Length: 1,056 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase C
EC: 3.2.1.8
UniProt: O69230
Ligands: CA
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Endo-1,4-beta-xylanase C (EC 3.2.1.8)	protein	352	41% helix, 17% strand	O69230

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	479	0.61	0.76	69	empty
2	476	0.60	0.75	69	empty
3	332	0.58	0.77	48	GOL
4	312	0.57	0.77	47	GOL
5	333	0.57	0.76	49	GOL

Interfaces

3 interfaces between chains.

A–B · 297 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 278 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 156 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4W8L · Structure of GH10 from Paenibacillus barci nsis · the same entry in another collection · chain A against A, TM-score 1.00
O69230 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase C (O69230) · 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 O69230
Elsewhere: RCSB PDB 4W8L · PDBe 4W8L · UniProt O69230

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