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Cryoem structure of zebra fish alpha-1 glycine receptor bound with taurine in sma, closed state
Analyse Cryoem structure of zebra fish alpha-1 glycine receptor bound with taurine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PM3
- Type
- protein
- Length
- 1,725 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- TAU, NAG
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 345 | 34% helix, 28% strand | O93430 |
Ligands and binding sites
- TAU · 2-aminoethanesulfonic acid · ligand · 5 copies · chains A, E, B, C, D
- 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
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.82 | 0.93 | 40 | empty |
| 2 | 457 | 0.75 | 0.84 | 60 | empty |
| 3 | 451 | 0.70 | 0.81 | 47 | empty |
| 4 | 440 | 0.70 | 0.81 | 48 | empty |
| 5 | 475 | 0.69 | 0.80 | 56 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2812 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 2807 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2806 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2806 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2804 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6PM3 · CryoEM structure of zebra fish alpha-1 glycine receptor bound with Taurine in SMA, closed… · 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 C against A, TM-score 0.93
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 6PM3 · PDBe 6PM3 · UniProt O93430
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