MolNFT v1 · #65248 · protein
Crystal structure of the F87M/L110M mutant of human transthyretin at pH 7.5
3GRG: “Crystal structure of the F87M/L110M mutant of human transthyretin at pH 7.5”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.57). MolNFT v1 #65248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GRG
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transthyretin | protein | 116 | 3% helix, 52% strand | P02766 |
| B, D, C | Transthyretin | protein | 115 | 3% helix, 52% strand | P02766 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 7 copies · chains A, B, D, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.57 | 0.80 | 34 | empty |
| 2 | 216 | 0.53 | 0.77 | 35 | empty |
| 3 | 135 | 0.49 | 0.79 | 29 | ACT |
| 4 | 77 | 0.34 | 0.75 | 19 | empty |
| 5 | 70 | 0.34 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 837 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 829 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3GRG · Crystal structure of the F87M/L110M mutant of human transthyretin at pH 7.5 · 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 3GRG · PDBe 3GRG · UniProt P02766
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