MolNFT v1 · #72404 · protein
Crystal structure of odorant binding protein 1 from anopheles gambiae (AGAMOBP1) with deet (N,N-diethyl-meta-toluamide) and peg
3N7H: “Crystal structure of odorant binding protein 1 from anopheles gambiae (AGAMOBP1) with deet…”. X-ray diffraction, 4 ligands (DE3, PEU, MG), 2 pockets (best druggability 0.87). MolNFT v1 #72404 on GenesisL1: 3D structure, binding…
- PDB
- 3N7H
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Odorant binding protein
- UniProt
- Q8T6S0
- Ligands
- DE3, PEU, MG, CL
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Odorant binding protein | protein | 125 | 58% helix, 2% strand | Q8T6S0 |
Ligands and binding sites
- DE3 · N,N-diethyl-3-methylbenzamide · ligand · 2 copies · chains A, B
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- MOH · Methanol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.87 | 0.92 | 66 | DE3, PEU |
| 2 | 125 | 0.43 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 707 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3N7H · Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with… · 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
- Every structure of UniProt Q8T6S0
- Elsewhere: RCSB PDB 3N7H · PDBe 3N7H · UniProt Q8T6S0
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