MolNFT v1 · #106195 · protein

Crystal structure of apo murine H90W cyclooxygenase-2

4RRY · Prostaglandin G/H synthase 2: “Crystal structure of apo murine H90W cyclooxygenase-2”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #106195 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4RRY
Type: protein
Length: 2,208 residues
Chains: 4
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: NAG
Pockets: 20 · best druggability 0.81

Structure

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

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

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	802	0.81	0.84	96	BOG
2	885	0.80	0.83	105	empty
3	671	0.80	0.85	64	empty
4	1075	0.80	0.81	105	empty
5	1013	0.79	0.81	95	empty

Interfaces

3 interfaces between chains.

C–D · 2631 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 2628 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 437 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

4RRY · Crystal Structure of Apo Murine H90W Cyclooxygenase-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 4RRY · PDBe 4RRY · UniProt Q05769

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