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Structure of ester-hydrolase EH7 from the metagenome of marine sediments at milazzo harbor (sicily, italy) complexed with a derivative of octyl 4-nitrophenyl hexylphosphonate

Analyse Structure of ester-hydrolase EH7 from the metagenome of marine sediments at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PU6
Type: protein
Length: 3,216 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase
UniProt: A0A2K8JQ66
Ligands: P8K
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Esterase	protein	402	34% helix, 22% strand	A0A2K8JQ66

Ligands and binding sites

P8K · hexyl(octoxy)phosphinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · chains B

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

Pockets

20 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	878	0.77	0.80	98	P8K
2	948	0.77	0.79	106	P8K
3	852	0.76	0.79	96	P8K
4	1117	0.76	0.78	131	P8K
5	966	0.76	0.78	121	P8K

Interfaces

12 interfaces between chains.

E–F · 1072 Å² buried · 12 hydrogen bonds · protein-protein
F–H · 1071 Å² buried · 15 hydrogen bonds · protein-protein
E–G · 1069 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1067 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1067 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

7PU6 · Structure of ester-hydrolase EH7 from the metagenome of marine sediments at milazzo… · 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 A0A2K8JQ66
Elsewhere: RCSB PDB 7PU6 · PDBe 7PU6 · UniProt A0A2K8JQ66

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