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Crystal Structure Of Sea Bream Transthyretin in complex with 3,5,6-trichloro-2-pyridinol (TC2P)
Analyse Crystal Structure Of Sea Bream Transthyretin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GNP
- Type
- protein
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.019
- Source
- Sparus aurata
- Molecule
- Transthyretin
- UniProt
- Q9PTT3
- Ligands
- F4Z
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.019 · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Transthyretin | protein | 114 | 5% helix, 50% strand | Q9PTT3 |
| B | Transthyretin | protein | 115 | 7% helix, 50% strand | Q9PTT3 |
Ligands and binding sites
- F4Z · 3,5,6-trichloro-2-pyridinol · 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 | 271 | 0.65 | 0.82 | 38 | F4Z |
| 2 | 286 | 0.64 | 0.81 | 37 | F4Z |
| 3 | 85 | 0.39 | 0.77 | 18 | empty |
| 4 | 81 | 0.37 | 0.76 | 16 | empty |
| 5 | 68 | 0.31 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 952 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GNP · Crystal structure of sea bream transthyretin in complex with 3,5,6- trichloro-2-pyridinol… · 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 6GNP · PDBe 6GNP · UniProt Q9PTT3
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