Research workbench
Crystal structure of dacm F87M/L110M transthyretin mutant
Analyse Crystal structure of dacm F87M/L110M transthyretin mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LLV
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transthyretin | protein | 116 | 6% helix, 53% strand | P02766 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 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 | 500 | 0.78 | 0.85 | 73 | ACT |
| 2 | 237 | 0.66 | 0.83 | 39 | empty |
| 3 | 79 | 0.38 | 0.77 | 19 | empty |
| 4 | 63 | 0.30 | 0.74 | 12 | empty |
| 5 | 62 | 0.29 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 899 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 885 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 462 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LLV · Crystal structure of DACM F87M/L110M Transthyretin mutant · 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 5LLV · PDBe 5LLV · UniProt P02766
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