Research workbench
Crystal structure of a trafficking protein particle complex subunit 3 from naegleria fowleri covalently bound to palmitic acid
Analyse Crystal structure of a trafficking protein particle complex subunit 3 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQ3
- Type
- protein
- Length
- 1,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trafficking protein particle complex subunit 3
- Ligands
- PLM
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trafficking protein particle complex subunit 3 | protein | 166 | 55% helix, 17% strand | — |
| B | Trafficking protein particle complex subunit 3 | protein | 171 | 51% helix, 16% strand | — |
| C | Trafficking protein particle complex subunit 3 | protein | 167 | 53% helix, 17% strand | — |
| D | Trafficking protein particle complex subunit 3 | protein | 170 | 54% helix, 16% strand | — |
| E | Trafficking protein particle complex subunit 3 | protein | 171 | 51% helix, 17% strand | — |
| F | Trafficking protein particle complex subunit 3 | protein | 169 | 53% helix, 17% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 6 copies · chains A, C, B, D, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.84 | 0.98 | 26 | PLM |
| 2 | 189 | 0.84 | 0.97 | 27 | PLM |
| 3 | 185 | 0.83 | 0.97 | 26 | PLM |
| 4 | 173 | 0.83 | 0.97 | 26 | PLM |
| 5 | 172 | 0.81 | 0.95 | 26 | PLM |
Interfaces
6 interfaces between chains.
- B–D · 1415 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1359 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1197 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 681 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 403 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 lipid (palmitoylation).
Compared structures
- 6AQ3 · Crystal structure of a trafficking protein particle complex subunit 3 from Naegleria… · 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 6AQ3 · PDBe 6AQ3
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