Research workbench
Rat transthyretin (also called prealbumin) complex with 3,3',5,5'- tetraiodothyroacetic acid (T4AC)
Analyse Rat transthyretin (also called prealbumin) complex with 3,3',5,5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KGI
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02767
- Ligands
- T4A
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Transthyretin | protein | 120 | 6% helix, 51% strand | P02767 |
| C | Transthyretin | protein | 121 | 5% helix, 49% strand | P02767 |
Ligands and binding sites
- T4A · 3,3',5,5'-tetraiodothyroacetic acid · ligand · 2 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.73 | 0.96 | 29 | empty |
| 2 | 331 | 0.71 | 0.84 | 38 | T4A |
| 3 | 364 | 0.66 | 0.80 | 49 | T4A |
| 4 | 75 | 0.37 | 0.77 | 16 | empty |
| 5 | 56 | 0.35 | 0.79 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 975 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 459 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1KGI · Rat transthyretin (also called prealbumin) complex with 3,3',5,5'-tetraiodothyroacetic… · the same entry in another collection · chain A against A, TM-score 1.00
- P02767 · AlphaFold monomer V2.0 prediction for transthyretin (P02767) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P02767
- Elsewhere: RCSB PDB 1KGI · PDBe 1KGI · UniProt P02767
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