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Structure of the engineered metalloesterase MID1SC9

Analyse Structure of the engineered metalloesterase MID1SC9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OD9
Type: protein
Length: 183 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MID1SC9
Ligands: 9RW, ZN, MG, CL
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MID1SC9	protein	95	82% helix, 0% strand	—
B	MID1SC9	protein	88	91% helix, 0% strand	—

Ligands and binding sites

9RW · (2~{S})-2-phenylpropanoic acid · ligand · chains A
ZN · Zinc ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
IMD · Imidazole · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.74	0.98	19	ZN, CL, EDO
2	97	0.59	0.87	23	IMD

Interfaces

1 interface between chains.

A–B · 779 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5OD9 · Structure of the engineered metalloesterase MID1sc9 · 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 5OD9 · PDBe 5OD9

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