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Crystal structure of a class V chitinase from arabidopsis thaliana

Analyse Crystal structure of a class V chitinase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AQU
Type: protein
Length: 1,376 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AT4G19810
EC: 3.2.1.14
UniProt: O81862
Pockets: 12 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	AT4G19810 (EC 3.2.1.14)	protein	344	38% helix, 26% strand	O81862

Ligands and binding sites

FLC · Citrate anion · additive · 3 copies · chains A, B

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

Pockets

12 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	450	0.61	0.76	78	empty
2	250	0.52	0.76	32	empty
3	187	0.49	0.77	28	empty
4	160	0.48	0.77	18	empty
5	213	0.47	0.74	38	empty

Interfaces

5 interfaces between chains.

B–D · 585 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 358 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 195 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 148 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 107 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3AQU · Crystal structure of a class V chitinase from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
O81862 · AlphaFold monomer V2.0 prediction for class V chitinase (O81862) · a predicted model of the same protein · chain C 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 O81862
Elsewhere: RCSB PDB 3AQU · PDBe 3AQU · UniProt O81862

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