MolNFT v1 · #123805 · protein

Crystal structure of S121P murine COX-2 mutant

5JVY · Prostaglandin G/H synthase 2: “Crystal structure of S121P murine COX-2 mutant”. X-ray diffraction, 4 ligands (COH, AKR, NAG), 8 pockets (best druggability 0.83). MolNFT v1 #123805 on GenesisL1: 3D structure, binding sites and…

PDB: 5JVY
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, NAG, MAN
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 46% 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	46% 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
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar
BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

8 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	846	0.83	0.85	92	empty
2	970	0.81	0.82	84	empty
3	693	0.79	0.84	64	empty
4	409	0.78	0.87	54	empty
5	444	0.77	0.85	56	empty

Interfaces

1 interface between chains.

A–B · 2759 Å² buried · 50 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

5JVY · Crystal structure of S121P murine COX-2 mutant · 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 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 Q05769
Elsewhere: RCSB PDB 5JVY · PDBe 5JVY · UniProt Q05769

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