Research workbench

Mcsg APC5046 probable glutaminase ybas

Analyse Mcsg APC5046 probable glutaminase ybas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U60
Type: protein
Length: 1,236 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable glutaminase ybas
EC: 3.5.1.2
UniProt: P77454
Pockets: 12 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Probable glutaminase ybas (EC 3.5.1.2)	protein	309	50% helix, 13% strand	P77454

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
FMT · Formic acid · additive · 9 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.63	0.80	48	EDO
2	586	0.63	0.75	53	empty
3	266	0.62	0.80	44	EDO, FMT
4	292	0.62	0.80	51	EDO
5	196	0.58	0.81	28	empty

Interfaces

3 interfaces between chains.

A–B · 1622 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1557 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 288 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1U60 · MCSG APC5046 Probable glutaminase ybaS · the same entry in another collection · chain A against A, TM-score 1.00
P77454 · AlphaFold monomer V2.0 prediction for glutaminase 1 (P77454) · a predicted model of the same protein · 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 P77454
Elsewhere: RCSB PDB 1U60 · PDBe 1U60 · UniProt P77454

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