MolNFT v1 · #168018 · protein
Cryoem structure of GABAB1B homodimer
6W2Y · Gamma-aminobutyric acid type B receptor subunit 1: “Cryoem structure of GABAB1B homodimer”. Electron microscopy, 4 ligands (L9Q, SGG, NAG), 16 pockets (best druggability 0.86). MolNFT v1 #168018 on GenesisL1: 3D structure, binding…
- PDB
- 6W2Y
- Type
- protein
- Length
- 1,327 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid type B receptor subunit 1
- UniProt
- Q9UBS5
- Ligands
- L9Q, SGG, NAG, MG
- Pockets
- 16 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-aminobutyric acid type B receptor subunit 1 | protein | 663 | 45% helix, 16% strand | Q9UBS5 |
| B | Gamma-aminobutyric acid type B receptor subunit 1 | protein | 664 | 46% helix, 14% strand | Q9UBS5 |
Ligands and binding sites
- L9Q · (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
- SGG · [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl) ethyl]amino]-2-oxidanyl-propyl]-(phenylmethyl) phosphinic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.86 | 0.89 | 66 | L9Q |
| 2 | 776 | 0.85 | 0.88 | 63 | L9Q |
| 3 | 415 | 0.68 | 0.80 | 61 | empty |
| 4 | 525 | 0.66 | 0.78 | 47 | empty |
| 5 | 325 | 0.62 | 0.78 | 38 | SGG |
Interfaces
1 interface between chains.
- A–B · 1688 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
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 Q9UBS5
- Elsewhere: RCSB PDB 6W2Y · PDBe 6W2Y · UniProt Q9UBS5
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