Research workbench

Dfp-inhibited esterase estb from burkholderia gladioli

Analyse Dfp-inhibited esterase estb from burkholderia gladioli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CI9
Type: protein
Length: 754 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (carboxylesterase)
EC: 3.1.1.1
UniProt: Q9KX40
Ligands: DFP
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (carboxylesterase) (EC 3.1.1.1)	protein	377	37% helix, 19% strand	Q9KX40

Ligands and binding sites

DFP · Diisopropyl phosphonate · ligand · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	389	0.75	0.85	65	DFP
2	367	0.73	0.84	63	DFP
3	336	0.62	0.79	27	empty
4	240	0.57	0.78	29	empty
5	298	0.53	0.75	30	empty

Interfaces

1 interface between chains.

A–B · 492 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1CI9 · Dfp-inhibited esterase estb from burkholderia gladioli · the same entry in another collection · chain A against A, TM-score 1.00
Q9KX40 · AlphaFold monomer V2.0 prediction for esterase estb (Q9KX40) · 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 Q9KX40
Elsewhere: RCSB PDB 1CI9 · PDBe 1CI9 · UniProt Q9KX40

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