MolNFT v1 · #149008 · protein
Structure of human BRAG2 (SEC7-pH domains) with the inhibitor bragsin bound to the pH domain
6FNE · Iq motif and SEC7 domain-containing protein 1: “Structure of human BRAG2 (SEC7-pH domains) with the inhibitor bragsin bound to the pH domain”. X-ray diffraction, 1 ligand (DY5), 5 pockets (best druggability 0.71). MolNFT v1 #149008…
- PDB
- 6FNE
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iq motif and SEC7 domain-containing protein 1
- UniProt
- Q6DN90
- Ligands
- DY5
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iq motif and SEC7 domain-containing protein 1 | protein | 350 | 46% helix, 16% strand | Q6DN90 |
| B | Iq motif and SEC7 domain-containing protein 1 | protein | 334 | 47% helix, 16% strand | Q6DN90 |
Ligands and binding sites
- DY5 · (2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one · ligand · chains A
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.71 | 0.78 | 74 | empty |
| 2 | 165 | 0.48 | 0.77 | 25 | empty |
| 3 | 169 | 0.47 | 0.76 | 25 | empty |
| 4 | 69 | 0.39 | 0.79 | 19 | empty |
| 5 | 52 | 0.32 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 869 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6FNE · Structure of human Brag2 (Sec7-PH domains) with the inhibitor Bragsin bound to the PH… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6DN90 · AlphaFold monomer V2.0 prediction for iq motif and SEC7 domain- containing protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q6DN90
- Elsewhere: RCSB PDB 6FNE · PDBe 6FNE · UniProt Q6DN90
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.