MolNFT v1 · #160497 · protein
Cryoem structure of zebra fish alpha-1 glycine receptor bound with glycine in sma, super-open state
6PM4 · Glycine receptor subunit ALPHAZ1: “Cryoem structure of zebra fish alpha-1 glycine receptor bound with glycine in sma, super-open state”. Electron microscopy, 3 ligands (GLY, NAG, BMA), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6PM4
- Type
- protein
- Length
- 1,730 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit ALPHAZ1
- UniProt
- O93430
- Ligands
- GLY, NAG, BMA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycine receptor subunit ALPHAZ1 | protein | 346 | 38% helix, 26% strand | O93430 |
Ligands and binding sites
- GLY · Glycine · 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
- BMA · beta-D-mannopyranose · sugar · 5 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.78 | 0.80 | 59 | empty |
| 2 | 719 | 0.75 | 0.80 | 96 | empty |
| 3 | 506 | 0.70 | 0.80 | 67 | empty |
| 4 | 372 | 0.70 | 0.82 | 47 | empty |
| 5 | 359 | 0.70 | 0.82 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2283 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2269 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2267 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2239 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2223 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6PM4 · CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in SMA… · 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 0.97
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 6PM4 · PDBe 6PM4 · UniProt O93430
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