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Structure of (R)-naproxen bound to mcox-2.

Analyse Structure of (R)-naproxen bound to mcox-2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q7D
Type: protein
Length: 1,104 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: HEM, NPX, NAG, CL
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Prostaglandin G/H synthase 2 (EC 1.14.99.1)	protein	552	47% helix, 8% strand	Q05769

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NPX · (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B

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

Pockets

12 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	757	0.82	0.85	87	empty
2	722	0.81	0.85	79	empty
3	1041	0.79	0.80	90	NPX, BOG
4	339	0.78	0.88	47	NPX, BOG, CL
5	474	0.76	0.85	56	empty

Interfaces

1 interface between chains.

A–B · 2588 Å² buried · 49 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3Q7D · Structure of (R)-naproxen bound to mCOX-2. · the same entry in another collection · chain A against A, 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 3Q7D · PDBe 3Q7D · UniProt Q05769

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