MolNFT v1 · #118825 · protein

Murine COX-2 S530T mutant

5FDQ · Prostaglandin G/H synthase 2: “Murine COX-2 S530T mutant”. X-ray diffraction, 5 ligands (COH, AKR, 60A), 10 pockets (best druggability 0.84). MolNFT v1 #118825 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FDQ
Type: protein
Length: 1,102 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prostaglandin G/H synthase 2
EC: 1.14.99.1
UniProt: Q05769
Ligands: COH, AKR, 60A, NAG, MAN
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Prostaglandin G/H synthase 2 (EC 1.14.99.1)	protein	551	48% helix, 9% strand	Q05769

Ligands and binding sites

COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
AKR · Acrylic acid · ligand · 2 copies · chains A, B
60A · 2-[(2~{R})-2-(hydroxymethyloxy)propoxy]ethanol · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · chains B
BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

10 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	918	0.84	0.85	106	60A
2	691	0.79	0.84	64	empty
3	352	0.79	0.89	45	empty
4	354	0.79	0.88	48	60A
5	409	0.78	0.87	53	empty

Interfaces

1 interface between chains.

A–B · 2646 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 7 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand, glycosylation).

Compared structures

5FDQ · Murine COX-2 S530T mutant · the same entry in another collection · chain B against B, TM-score 1.00
Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · a predicted model of the same protein · 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 Q05769
Elsewhere: RCSB PDB 5FDQ · PDBe 5FDQ · UniProt Q05769

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