MolNFT v1 · #160890 · protein
Cryoem structure of zebra fish alpha-1 glycine receptor, apo state
6PXD · Glycine receptor subunit ALPHAZ1: “Cryoem structure of zebra fish alpha-1 glycine receptor, apo state”. Electron microscopy, 2 ligands (NAG, CL), 20 pockets (best druggability 0.80). MolNFT v1 #160890 on GenesisL1: 3D structure…
- PDB
- 6PXD
- Type
- protein
- Length
- 1,700 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- NAG, CL
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, B, C, D | Glycine receptor subunit ALPHAZ1 | protein | 340 | 35% helix, 28% strand | O93430 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains E, A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains E, A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.80 | 0.87 | 47 | CL |
| 2 | 404 | 0.79 | 0.88 | 40 | CL |
| 3 | 450 | 0.76 | 0.85 | 54 | empty |
| 4 | 422 | 0.75 | 0.85 | 48 | empty |
| 5 | 528 | 0.74 | 0.82 | 50 | empty |
Interfaces
5 interfaces between chains.
- E–D · 2618 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2603 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2602 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2600 Ų buried · 18 hydrogen bonds · protein-protein
- E–A · 2598 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6PXD · CryoEM structure of zebra fish alpha-1 glycine receptor, Apo state · the same entry in another collection · chain D against D, TM-score 1.00
- O93430 · AlphaFold monomer V2.0 prediction for glycine receptor subunit ALPHAZ1 (O93430) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 6PXD · PDBe 6PXD · UniProt O93430
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