MolNFT v1 · #9338 · protein
The 2.7 ångström resolution model of ovine COX-1 complexed with alclofenac
1HT8 · Prostaglandin H2 synthase-1: “The 2.7 ångström resolution model of ovine COX-1 complexed with alclofenac”. X-ray diffraction, 3 ligands (HEM, 34C, NAG), 8 pockets (best druggability 0.85). MolNFT v1 #9338 on GenesisL1: 3D structure…
- PDB
- 1HT8
- Type
- protein
- Length
- 1,102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin H2 synthase-1
- EC
- 1.14.99.1
- UniProt
- P05979
- Ligands
- HEM, 34C, NAG
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin H2 synthase-1 (EC 1.14.99.1) | protein | 551 | 46% helix, 9% strand | P05979 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 34C · (3-chloro-4-propoxy-phenyl)-acetic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.85 | 0.86 | 124 | BOG, 34C |
| 2 | 1163 | 0.83 | 0.84 | 118 | BOG, 34C |
| 3 | 550 | 0.77 | 0.84 | 60 | empty |
| 4 | 458 | 0.68 | 0.79 | 36 | HEM |
| 5 | 453 | 0.66 | 0.78 | 38 | HEM |
Interfaces
1 interface between chains.
- A–B · 2631 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1HT8 · The 2.7 ångström resolution model of ovine COX-1 complexed with alclofenac · the same entry in another collection · chain A against A, TM-score 1.00
- P05979 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 1 (P05979) · 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 P05979
- Elsewhere: RCSB PDB 1HT8 · PDBe 1HT8 · UniProt P05979
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