Research workbench
Crystal structure of sea bream transthyretin in complex with perfluorooctanoic acid (pfoa). crystallized in peg
Analyse Crystal structure of sea bream transthyretin in complex with perfluorooctanoic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GON
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- Q9PTT3
- Ligands
- 8PF
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transthyretin | protein | 114 | 9% helix, 48% strand | Q9PTT3 |
| C, D | Transthyretin | protein | 115 | 10% helix, 51% strand | Q9PTT3 |
Ligands and binding sites
- 8PF · pentadecafluorooctanoic acid · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.67 | 0.83 | 29 | 8PF |
| 2 | 274 | 0.65 | 0.81 | 28 | 8PF |
| 3 | 112 | 0.41 | 0.76 | 19 | empty |
| 4 | 87 | 0.38 | 0.76 | 19 | empty |
| 5 | 89 | 0.36 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 956 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 946 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 401 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GON · Crystal Structure Of Sea Bream Transthyretin in complex with Perfluorooctanoic acid… · 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 Q9PTT3
- Elsewhere: RCSB PDB 6GON · PDBe 6GON · UniProt Q9PTT3
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