MolNFT v1 · #188498 · protein
Cryo-EM structure of GSK682753A-bound EBI2/GPR183
7TUY · Anti-bril Fab heavy chain: “Cryo-EM structure of GSK682753A-bound EBI2/GPR183”. Electron microscopy, 1 ligand (KKF), 10 pockets (best druggability 0.81). MolNFT v1 #188498 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7TUY
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-bril Fab heavy chain; Anti-Fab nanobody; Anti-bril Fab light chain; G-protein…
- UniProt
- P32249
- Ligands
- KKF
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-bril Fab heavy chain | protein | 225 | 6% helix, 45% strand | — |
| K | Anti-Fab nanobody | protein | 120 | 0% helix, 41% strand | — |
| L | Anti-bril Fab light chain | protein | 212 | 4% helix, 46% strand | — |
| R | G-protein coupled receptor 183,SOLUBLE cytochrome B562 fusion | protein | 371 | 75% helix, 0% strand | P32249 |
Ligands and binding sites
- KKF · 8-[(2E)-3-(4-chlorophenyl)prop-2-enoyl]-3-[(3,4-dichlorophenyl)methyl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.81 | 0.84 | 65 | KKF |
| 2 | 205 | 0.52 | 0.77 | 29 | empty |
| 3 | 261 | 0.50 | 0.75 | 46 | empty |
| 4 | 66 | 0.49 | 0.84 | 17 | empty |
| 5 | 88 | 0.44 | 0.80 | 18 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1942 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 690 Ų buried · 8 hydrogen bonds · protein-protein
- L–R · 495 Ų buried · 2 hydrogen bonds · protein-protein
- H–R · 346 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 P32249
- Elsewhere: RCSB PDB 7TUY · PDBe 7TUY · UniProt P32249
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