Research workbench
Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, strychnine bound state
Analyse Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, strychnine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KUY
- Type
- protein
- Length
- 1,694 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine receptor subunit alpha-2; Glycine receptor subunit beta, green fluorescent…
- UniProt
- P23416, P48167
- Ligands
- SY9, NAG
- Pockets
- 17 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine receptor subunit alpha-2 | protein | 339 | 35% helix, 27% strand | P23416 |
| E | Glycine receptor subunit beta, green fluorescent protein chimera | protein | 338 | 30% helix, 27% strand | P48167 |
Ligands and binding sites
- SY9 · Strychnine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.81 | 0.83 | 93 | SY9 |
| 2 | 853 | 0.79 | 0.82 | 92 | empty |
| 3 | 678 | 0.77 | 0.82 | 67 | SY9 |
| 4 | 958 | 0.77 | 0.79 | 94 | SY9 |
| 5 | 621 | 0.76 | 0.82 | 67 | SY9 |
Interfaces
7 interfaces between chains.
- B–C · 2589 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2533 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2511 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2506 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2386 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KUY · Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state · the same entry in another collection · chain E against E, TM-score 1.00
- P23416 · AlphaFold monomer V2.0 prediction for glycine receptor subunit alpha-2 (P23416) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P48167 · AlphaFold monomer V2.0 prediction for glycine receptor subunit beta (P48167) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 P23416
- Every structure of UniProt P48167
- Elsewhere: RCSB PDB 7KUY · PDBe 7KUY · UniProt P23416 · UniProt P48167
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.