Research workbench
Crystal structure of V30M mutated transthyretin in complex with alpha- mangostin
Analyse Crystal structure of V30M mutated transthyretin in complex with alpha- mangostin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y9B
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- MKS, CA, CL
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transthyretin | protein | 116 | 6% helix, 51% strand | P02766 |
| B | Transthyretin | protein | 115 | 6% helix, 51% strand | P02766 |
Ligands and binding sites
- MKS · 1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.37 | 0.76 | 16 | empty |
| 2 | 92 | 0.36 | 0.75 | 16 | empty |
| 3 | 63 | 0.26 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 917 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4Y9B · Crystal structure of V30M mutated transthyretin in complex with alpha-mangostin · 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 P02766
- Elsewhere: RCSB PDB 4Y9B · PDBe 4Y9B · UniProt P02766
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