MolNFT v1 · #103883 · protein

Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus vulgaris in complex with K+ cations

4PU6 · L-asparaginase alpha subunit: “Crystal structure of potassium-dependent plant-type L-asparaginase from phaseolus vulgaris in complex with K+…”. X-ray diffraction, 2 ligands (ASP, K), 4 pockets (best druggability 0.64). MolNFT v1…

PDB: 4PU6
Type: protein
Length: 576 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase alpha subunit; L-asparaginase beta subunit
EC: 3.5.1.1
UniProt: V7CU13
Ligands: ASP, K
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	L-asparaginase alpha subunit (EC 3.5.1.1)	protein	157	49% helix, 18% strand	V7CU13
B, D	L-asparaginase beta subunit (EC 3.5.1.1)	protein	131	21% helix, 37% strand	V7CU13

Ligands and binding sites

ASP · Aspartic acid · ligand · chains A, B
K · Potassium ion · metal · 4 copies · chains A, C

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

Pockets

4 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	452	0.64	0.77	39	empty
2	351	0.60	0.77	38	ASP
3	80	0.32	0.74	18	empty
4	57	0.26	0.73	17	K

Interfaces

6 interfaces between chains.

C–D · 2845 Å² buried · 60 hydrogen bonds · protein-protein
A–B · 2843 Å² buried · 57 hydrogen bonds · protein-protein
B–D · 603 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 599 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 598 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4PU6 · Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus… · the same entry in another collection · chain A 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 V7CU13
Elsewhere: RCSB PDB 4PU6 · PDBe 4PU6 · UniProt V7CU13

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