Research workbench
Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, glycine bound, (SEMI)OPEN state
Analyse Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, glycine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BKG
- Type
- protein
- Length
- 1,686 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 protein
- UniProt
- P23416, P48167, P42212
- Ligands
- GLY, NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine receptor subunit alpha-2 | protein | 338 | 35% helix, 28% strand | P23416 |
| E | Glycine receptor subunit BETA,GREEN fluorescent protein | protein | 334 | 32% helix, 27% strand | P48167, P42212 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A, E, B, C
- 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
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 | 1126 | 0.82 | 0.83 | 117 | empty |
| 2 | 347 | 0.71 | 0.84 | 48 | empty |
| 3 | 87 | 0.69 | 0.93 | 26 | empty |
| 4 | 507 | 0.69 | 0.80 | 50 | empty |
| 5 | 343 | 0.69 | 0.82 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2643 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2587 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 2576 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2553 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2424 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 5BKG · Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, glycine bound… · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.98
- 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 0.97
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain E against A, TM-score 0.22
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
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 5BKG · PDBe 5BKG · UniProt P23416 · UniProt P48167 · UniProt P42212
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