MolNFT v1 · #92620 · protein
Structure of the tryptamine complex of the amine binding protein of rhodnius prolixus
4GE1 · Biogenic amine-binding protein: “Structure of the tryptamine complex of the amine binding protein of rhodnius prolixus”. X-ray diffraction, 1 ligand (TSS), 12 pockets (best druggability 0.75). MolNFT v1 #92620 on GenesisL1: 3D…
- PDB
- 4GE1
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biogenic amine-binding protein
- UniProt
- Q86PT9
- Ligands
- TSS
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biogenic amine-binding protein | protein | 195 | 21% helix, 42% strand | Q86PT9 |
| B | Biogenic amine-binding protein | protein | 194 | 21% helix, 40% strand | Q86PT9 |
| C | Biogenic amine-binding protein | protein | 193 | 25% helix, 39% strand | Q86PT9 |
| D | Biogenic amine-binding protein | protein | 194 | 23% helix, 39% strand | Q86PT9 |
Ligands and binding sites
- TSS · 2-(1H-indol-3-yl)ethanamine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.75 | 0.83 | 57 | empty |
| 2 | 324 | 0.72 | 0.84 | 33 | TSS |
| 3 | 321 | 0.70 | 0.83 | 37 | TSS |
| 4 | 235 | 0.69 | 0.85 | 32 | TSS |
| 5 | 248 | 0.69 | 0.85 | 34 | TSS |
Interfaces
5 interfaces between chains.
- C–D · 680 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 667 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 238 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 154 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4GE1 · Structure of the tryptamine complex of the amine binding protein of Rhodnius prolixus · 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 Q86PT9
- Elsewhere: RCSB PDB 4GE1 · PDBe 4GE1 · UniProt Q86PT9
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