Research workbench
Crystal structure of sea bream transthyretin in complex with 2,4,5- trichlorophenoxyacetic acid (2,4,5-T)
Analyse Crystal structure of sea bream transthyretin in complex with 2,4,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GNW
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- Q9PTT3
- Ligands
- F52
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Transthyretin | protein | 115 | 6% helix, 50% strand | Q9PTT3 |
| B | Transthyretin | protein | 116 | 7% helix, 47% strand | Q9PTT3 |
Ligands and binding sites
- F52 · 2-[2,4,5-tris(chloranyl)phenoxy]ethanoic 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.64 | 0.81 | 32 | F52 |
| 2 | 272 | 0.64 | 0.81 | 34 | F52 |
| 3 | 89 | 0.37 | 0.76 | 18 | empty |
| 4 | 57 | 0.30 | 0.75 | 14 | empty |
| 5 | 60 | 0.27 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 943 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 406 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GNW · Crystal Structure Of Sea Bream Transthyretin in complex with 2,4,5-trichlorophenoxyacetic… · 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 6GNW · PDBe 6GNW · UniProt Q9PTT3
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