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Crystal structure of the first plant urease from jack bean (canavalia ensiformis)

Analyse Crystal structure of the first plant urease from jack bean (canavalia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LA4
Type: protein
Length: 837 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urease
EC: 3.5.1.5
UniProt: P07374
Ligands: ACN, NI, PO4
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urease (EC 3.5.1.5)	protein	837	29% helix, 23% strand	P07374

Ligands and binding sites

ACN · Acetone · ligand
NI · Nickel (II) ion · metal · 2 copies · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A

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	813	0.70	0.76	85	empty
2	122	0.50	0.80	24	NI, PO4
3	131	0.41	0.75	15	empty
4	76	0.32	0.74	22	empty
5	72	0.30	0.73	15	empty

Modifications

Observed in the structure: 4 modified (artifact, carboxylation).

Compared structures

3LA4 · Crystal structure of the first plant urease from Jack bean (Canavalia ensiformis) · the same entry in another collection · chain A against A, TM-score 1.00
P07374 · AlphaFold monomer V2.0 prediction for urease (P07374) · 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 P07374
Elsewhere: RCSB PDB 3LA4 · PDBe 3LA4 · UniProt P07374

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