MolNFT v1 · #72692 · protein
Crystal structure of V30M transthyretin complexed with (-)- epigallocatechin gallate (egcg)
3NG5: “Crystal structure of V30M transthyretin complexed with (-)- epigallocatechin gallate (egcg)”. X-ray diffraction, 1 ligand (KDH), 2 pockets (best druggability 0.35). MolNFT v1 #72692 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NG5
- Type
- protein
- Length
- 233 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transthyretin
- UniProt
- P02766
- Ligands
- KDH
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transthyretin | protein | 117 | 6% helix, 52% strand | P02766 |
| B | Transthyretin | protein | 116 | 6% helix, 53% strand | P02766 |
Ligands and binding sites
- KDH · (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate · ligand · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.35 | 0.78 | 16 | empty |
| 2 | 59 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3NG5 · Crystal Structure of V30M transthyretin complexed with (-)-epigallocatechin gallate (EGCG) · 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 3NG5 · PDBe 3NG5 · UniProt P02766
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