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Structure of an esterase from the oil-degrading bacterium oleispira antarctica

Analyse Structure of an esterase from the oil-degrading bacterium oleispira antarctica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3I6Y
Type: protein
Length: 556 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase APC40077
EC: 3.1.1.2
Ligands: CL
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Esterase APC40077 (EC 3.1.1.2)	protein	278	39% helix, 24% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	374	0.66	0.80	71	EDO, CL, PEG

Interfaces

1 interface between chains.

A–B · 984 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3I6Y · Structure of an esterase from the oil-degrading bacterium Oleispira antarctica · 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
Elsewhere: RCSB PDB 3I6Y · PDBe 3I6Y

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