MolNFT v1 · #150273 · protein
Crystal structure of sea bream transthyretin in complex with perfluorooctanoic acid (pfoa). crystallized in peg
6GON: “Crystal structure of sea bream transthyretin in complex with perfluorooctanoic acid (pfoa). crystallized in…”. X-ray diffraction, 1 ligand (8PF), 7 pockets (best druggability 0.67). MolNFT v1 #150273 on GenesisL1: 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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