MolNFT v1 · #83441 · protein
Crystal structure of anti-prostaglandin E2 Fab fragment 9CL-PGF2BETA complex
3WIF · Mab Fab H fragment: “Crystal structure of anti-prostaglandin E2 Fab fragment 9CL-PGF2BETA complex”. X-ray diffraction, 1 ligand (ON5), 4 pockets (best druggability 0.70). MolNFT v1 #83441 on GenesisL1: 3D structure, binding sites…
- PDB
- 3WIF
- 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
- ON5
- Pockets
- 4 · best druggability 0.70
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, 54% strand | — |
| B | Mab Fab L fragment | protein | 216 | 6% helix, 52% strand | — |
Ligands and binding sites
- ON5 · (Z)-7-[(1R,2R,3R,5R)-5-chloranyl-3-oxidanyl-2-[(E,3S)-3-oxidanyloct-1-enyl]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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.70 | 0.87 | 31 | ON5 |
| 2 | 526 | 0.61 | 0.75 | 53 | empty |
| 3 | 120 | 0.40 | 0.75 | 27 | empty |
| 4 | 62 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1767 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3WIF · Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2beta 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 3WIF · PDBe 3WIF
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