MolNFT v1 · #47867 · protein

Gsh-heme bound microsomal prostaglandin E synthase

2PBJ · Prostaglandin E synthase 2: “Gsh-heme bound microsomal prostaglandin E synthase”. X-ray diffraction, 3 ligands (HEM, GSH, CL), 13 pockets (best druggability 0.80). MolNFT v1 #47867 on GenesisL1: 3D structure, binding sites and…

PDB: 2PBJ
Type: protein
Length: 1,096 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prostaglandin E synthase 2
EC: 5.3.99.3
UniProt: Q9N0A4
Ligands: HEM, GSH, CL
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Prostaglandin E synthase 2 (EC 5.3.99.3)	protein	274	56% helix, 12% strand	Q9N0A4

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, D, B, C

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

Pockets

13 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	0.80	0.82	101	HEM, GSH
2	802	0.79	0.82	86	GSH
3	355	0.64	0.79	35	empty
4	230	0.63	0.82	29	HEM
5	202	0.63	0.82	29	HEM

Interfaces

5 interfaces between chains.

A–B · 1441 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1440 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 285 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 282 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 182 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2PBJ · GSH-heme bound microsomal prostaglandin E synthase · 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 2PBJ · PDBe 2PBJ · UniProt Q9N0A4

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