MolNFT v1 · #163159 · protein

Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-glu

6RUF: “Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-glu”. X-ray diffraction, 1 ligand (GLU), 11 pockets (best druggability 0.82). MolNFT v1 #163159 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RUF
Type: protein
Length: 1,274 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase
EC: 3.5.1.1
UniProt: P50286
Ligands: GLU
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	L-asparaginase (EC 3.5.1.1)	protein	319	33% helix, 21% strand	P50286
C	L-asparaginase (EC 3.5.1.1)	protein	317	34% helix, 22% strand	P50286

Ligands and binding sites

GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	584	0.82	0.87	88	empty
2	139	0.69	0.90	31	empty
3	57	0.68	0.97	29	empty
4	51	0.67	0.97	30	empty
5	82	0.65	0.92	21	empty

Interfaces

6 interfaces between chains.

A–B · 2085 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 2063 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 942 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 872 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6RUF · Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-Glu · the same entry in another collection · chain C against C, TM-score 1.00
P50286 · AlphaFold monomer V2.0 prediction for L-asparaginase (P50286) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P50286
Elsewhere: RCSB PDB 6RUF · PDBe 6RUF · UniProt P50286

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