MolNFT v1 · #110236 · protein

X-ray structure analysis of xylanase-wt at PH4.0

4XQD · Endo-1,4-beta-xylanase 2: “X-ray structure analysis of xylanase-wt at PH4.0”. X-ray diffraction, 1 ligand (IOD), 3 pockets (best druggability 0.58). MolNFT v1 #110236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XQD
Type: protein
Length: 377 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase 2
EC: 3.2.1.8
UniProt: P36217
Ligands: IOD
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endo-1,4-beta-xylanase 2 (EC 3.2.1.8)	protein	188	5% helix, 62% strand	P36217
B	Endo-1,4-beta-xylanase 2 (EC 3.2.1.8)	protein	189	5% helix, 61% strand	P36217

Ligands and binding sites

IOD · Iodide ion · ion · 6 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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	243	0.58	0.79	31	empty
2	293	0.56	0.76	34	empty
3	168	0.43	0.75	32	empty

Interfaces

1 interface between chains.

A–B · 141 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4XQD · X-ray structure analysis of xylanase-WT at pH4.0 · the same entry in another collection · chain A against A, TM-score 1.00
P36217 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase 2 (P36217) · 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 P36217
Elsewhere: RCSB PDB 4XQD · PDBe 4XQD · UniProt P36217

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