MolNFT v1 · #114332 · protein
Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, glycine bound, desensitized state
5BKF · Glycine receptor subunit alpha-2: “Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, glycine bound, desensitized state”. Electron microscopy, 2 ligands (GLY, NAG), 19 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5BKF
- Type
- protein
- Length
- 1,689 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
- 19 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine receptor subunit alpha-2 | protein | 338 | 36% helix, 25% strand | P23416 |
| E | Glycine receptor subunit BETA,GREEN fluorescent protein | protein | 337 | 33% helix, 24% strand | P48167, P42212 |
Ligands and binding sites
- GLY · Glycine · 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.80 | 0.82 | 84 | empty |
| 2 | 481 | 0.75 | 0.83 | 62 | empty |
| 3 | 449 | 0.69 | 0.81 | 56 | empty |
| 4 | 460 | 0.69 | 0.80 | 54 | empty |
| 5 | 437 | 0.68 | 0.80 | 52 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2658 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 2571 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2538 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2525 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2512 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5BKF · 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 C against A, TM-score 0.99
- 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 5BKF · PDBe 5BKF · UniProt P23416 · UniProt P48167 · UniProt P42212
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