Research workbench
Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex
Analyse Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WHX
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mab Fab H fragment; Mab Fab L fragment
- Ligands
- XPG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mab Fab H fragment | protein | 211 | 9% helix, 53% strand | — |
| B | Mab Fab L fragment | protein | 216 | 6% helix, 52% strand | — |
Ligands and binding sites
- XPG · 7-[(1R,3R)-3-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-5-oxocyclopentyl]heptanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.69 | 0.86 | 30 | XPG |
| 2 | 589 | 0.63 | 0.74 | 58 | empty |
| 3 | 71 | 0.49 | 0.84 | 21 | empty |
| 4 | 114 | 0.39 | 0.75 | 26 | empty |
| 5 | 52 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1668 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3WHX · Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3WHX · PDBe 3WHX
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