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Structure of the tryptamine complex of the amine binding protein of rhodnius prolixus
Analyse Structure of the tryptamine complex of the amine binding protein of rhodnius… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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