Research workbench
Crystal structure of anti-prostaglandin E2 Fab fragment PGE2 complex
Analyse Crystal structure of anti-prostaglandin E2 Fab fragment PGE2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFH
- 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
- P2E
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mab Fab H fragment | protein | 211 | 7% helix, 53% strand | — |
| B | Mab Fab L fragment | protein | 216 | 6% helix, 52% strand | — |
Ligands and binding sites
- P2E · (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic 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 | 202 | 0.70 | 0.87 | 30 | P2E |
| 2 | 591 | 0.63 | 0.75 | 54 | empty |
| 3 | 58 | 0.48 | 0.85 | 20 | empty |
| 4 | 117 | 0.40 | 0.75 | 25 | empty |
| 5 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1747 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3WFH · Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 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 3WFH · PDBe 3WFH
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