MolNFT v1 · #106288 · protein
Crystal structure of murine cyclooxygenase-2 with 13-methyl- arachidonic acid
4RUT · Prostaglandin G/H synthase 2: “Crystal structure of murine cyclooxygenase-2 with 13-methyl- arachidonic acid”. X-ray diffraction, 3 ligands (COH, LM8, NAG), 20 pockets (best druggability 0.82). MolNFT v1 #106288 on GenesisL1: 3D…
- PDB
- 4RUT
- 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
- COH, LM8, NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% 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, 9% strand | Q05769 |
Ligands and binding sites
- COH · Protoporphyrin IX containing co · ligand · 4 copies · chains A, B, C, D
- LM8 · (5Z,8Z,11Z,13S,14Z)-13-methylicosa-5,8,11,14-tetraenoic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains B, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.82 | 0.89 | 64 | LM8 |
| 2 | 419 | 0.82 | 0.90 | 60 | LM8 |
| 3 | 426 | 0.82 | 0.89 | 61 | LM8 |
| 4 | 1167 | 0.81 | 0.82 | 118 | empty |
| 5 | 542 | 0.81 | 0.86 | 72 | LM8 |
Interfaces
3 interfaces between chains.
- C–D · 2638 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2622 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4RUT · crystal structure of murine cyclooxygenase-2 with 13-methyl-arachidonic Acid · 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 4RUT · PDBe 4RUT · UniProt Q05769
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