MolNFT v1 · #103850 · protein
Crystal structure of locusta migratoria odorant binding proteins LMIGOBP1
4PT1 · Odorant-binding protein 1D: “Crystal structure of locusta migratoria odorant binding proteins LMIGOBP1”. X-ray diffraction, 4 pockets (best druggability 0.85). MolNFT v1 #103850 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4PT1
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Odorant-binding protein 1D
- UniProt
- Q3HM32
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Odorant-binding protein 1D | protein | 129 | 67% helix, 2% strand | Q3HM32 |
| B | Odorant-binding protein 1D | protein | 128 | 70% helix, 2% strand | Q3HM32 |
Ligands and binding sites
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 4 copies · 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 | 237 | 0.85 | 0.97 | 34 | PG0 |
| 2 | 234 | 0.85 | 0.97 | 31 | PG0 |
| 3 | 117 | 0.45 | 0.78 | 22 | empty |
| 4 | 70 | 0.42 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 272 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4PT1 · Crystal structure of Locusta migratoria odorant binding proteins lmigOBP1 · 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 Q3HM32
- Elsewhere: RCSB PDB 4PT1 · PDBe 4PT1 · UniProt Q3HM32
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