MolNFT v1 · #61262 · protein
Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6
3DGD: “Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.58). MolNFT v1 #61262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DGD
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transthyretin | protein | 116 | 0% helix, 52% strand | P02766 |
| B, D | Transthyretin | protein | 115 | 0% helix, 52% strand | P02766 |
Ligands and binding sites
- ZN · Zinc ion · metal · 15 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.58 | 0.79 | 33 | empty |
| 2 | 246 | 0.58 | 0.79 | 37 | empty |
| 3 | 174 | 0.52 | 0.78 | 26 | ACT, ZN, GOL |
| 4 | 86 | 0.36 | 0.76 | 23 | empty |
| 5 | 64 | 0.34 | 0.77 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 875 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 470 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 440 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3DGD · Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6 · 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 3DGD · PDBe 3DGD · UniProt P02766
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