MolNFT v1 · #54610 · protein

Natural product-guided discovery of a fungal chitinase inhibitor

2XUC: “Natural product-guided discovery of a fungal chitinase inhibitor”. X-ray diffraction, 3 ligands (XRG, PO4, CL), 5 pockets (best druggability 0.65). MolNFT v1 #54610 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XUC
Type: protein
Length: 913 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chitinase
EC: 3.2.1.14
UniProt: Q873Y0
Ligands: XRG, PO4, CL
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chitinase (EC 3.2.1.14)	protein	310	35% helix, 21% strand	Q873Y0
C	Chitinase (EC 3.2.1.14)	protein	293	30% helix, 19% strand	Q873Y0

Ligands and binding sites

XRG · 1-methyl-3-(N-methylcarbamimidoyl)urea · ligand · 5 copies · chains A, B, C
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.65	0.88	25	empty
2	71	0.38	0.78	21	XRG
3	80	0.36	0.76	21	XRG
4	50	0.30	0.76	16	XRG
5	55	0.28	0.74	13	empty

Interfaces

1 interface between chains.

A–C · 14 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

2XUC · Natural product-guided discovery of a fungal chitinase inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q873Y0 · AlphaFold monomer V2.0 prediction for endochitinase A1 (Q873Y0) · a predicted model of the same protein · chain B 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 Q873Y0
Elsewhere: RCSB PDB 2XUC · PDBe 2XUC · UniProt Q873Y0

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