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Microsomal prostaglandin E synthase type-2

Analyse Microsomal prostaglandin E synthase type-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Z9H
Type: protein
Length: 1,096 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Membrane-associated prostaglandin E synthase-2
EC: 5.3.99.3
UniProt: Q9N0A4
Ligands: IMN, CL
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Membrane-associated prostaglandin E synthase-2 (EC 5.3.99.3)	protein	274	57% helix, 12% strand	Q9N0A4

Ligands and binding sites

IMN · Indomethacin · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains B, C, A, D
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1093	0.80	0.81	111	ACT, IMN
2	655	0.75	0.81	57	empty
3	326	0.68	0.82	36	empty
4	320	0.67	0.82	36	empty
5	218	0.63	0.82	34	ACT, IMN

Interfaces

5 interfaces between chains.

A–B · 1539 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1537 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 264 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 264 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 184 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1Z9H · Microsomal prostaglandin E synthase type-2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9N0A4 · AlphaFold monomer V2.0 prediction for prostaglandin E synthase 2 (Q9N0A4) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9N0A4
Elsewhere: RCSB PDB 1Z9H · PDBe 1Z9H · UniProt Q9N0A4

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