MolNFT v1 · #165962 · protein
Full length glycine receptor reconstituted in lipid nanodisc in APO/RESTING conformation
6UBS · Glycine receptor subunit ALPHAZ1: “Full length glycine receptor reconstituted in lipid nanodisc in APO/RESTING conformation”. Electron microscopy, 3 ligands (PX4, PIO, NAG), 20 pockets (best druggability 0.81). MolNFT v1 #165962 on…
- PDB
- 6UBS
- Type
- protein
- Length
- 1,810 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- PX4, PIO, NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 362 | 37% helix, 25% strand | O93430 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 10 copies · chains A, B, C, D, E
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.81 | 0.82 | 107 | empty |
| 2 | 1012 | 0.80 | 0.82 | 101 | empty |
| 3 | 322 | 0.80 | 0.90 | 40 | empty |
| 4 | 1189 | 0.79 | 0.80 | 117 | empty |
| 5 | 1153 | 0.79 | 0.81 | 112 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2682 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2649 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2638 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2610 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2595 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 6UBS · Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation · the same entry in another collection · chain E against E, TM-score 1.00
- O93430 · AlphaFold monomer V2.0 prediction for glycine receptor subunit ALPHAZ1 (O93430) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 O93430
- Elsewhere: RCSB PDB 6UBS · PDBe 6UBS · UniProt O93430
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