MolNFT v1 · #117040 · protein

Crystal structure of esterase PE8

5DWD: “Crystal structure of esterase PE8”. X-ray diffraction, 1 ligand (1PG), 3 pockets (best druggability 0.65). MolNFT v1 #117040 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DWD
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase
EC: 3.1.1.1
UniProt: G4RFI7
Ligands: 1PG
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Esterase (EC 3.1.1.1)	protein	215	39% helix, 21% strand	G4RFI7
B	Esterase (EC 3.1.1.1)	protein	223	38% helix, 20% strand	G4RFI7

Ligands and binding sites

1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains B
GOL · Glycerol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.65	0.77	40	empty
2	69	0.34	0.75	15	empty
3	60	0.29	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 198 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5DWD · Crystal structure of esterase PE8 · 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 G4RFI7
Elsewhere: RCSB PDB 5DWD · PDBe 5DWD · UniProt G4RFI7

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