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Crystal structure of sortase B complexed with GLY3

Analyse Crystal structure of sortase B complexed with GLY3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QXA
Type: protein
Length: 217 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Npqtn specific sortase B; Peptide gly-gly-gly
UniProt: Q8NX63
Ligands: ETM
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Npqtn specific sortase B	protein	214	29% helix, 27% strand	Q8NX63
B	Peptide gly-gly-gly	protein	3	0% helix, 0% strand	—

Ligands and binding sites

ETM · 2-(trimethylammonium)ethyl thiol · ligand · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.36	0.80	17	empty
2	57	0.30	0.75	15	ETM

Interfaces

1 interface between chains.

A–B · 177 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1QXA · Crystal structure of Sortase B complexed with Gly3 · 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 Q8NX63
Elsewhere: RCSB PDB 1QXA · PDBe 1QXA · UniProt Q8NX63

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