MolNFT v1 · #180543 · protein
Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, strychnine bound state, 3.8 ångström
7L31 · Glycine receptor subunit alpha-2: “Cyro-EM structure of human glycine receptor ALPHA2-beta heteromer, strychnine bound state, 3.8 ångström”. Electron microscopy, 2 ligands (SY9, NAG), 19 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7L31
- 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
- Ligands
- SY9, NAG
- Pockets
- 19 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 33% helix, 28% 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 | protein | 330 | 32% helix, 29% 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
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.79 | 0.83 | 72 | SY9 |
| 2 | 829 | 0.78 | 0.82 | 77 | SY9 |
| 3 | 672 | 0.78 | 0.83 | 65 | SY9 |
| 4 | 733 | 0.77 | 0.81 | 63 | SY9 |
| 5 | 521 | 0.76 | 0.83 | 53 | SY9 |
Interfaces
6 interfaces between chains.
- A–B · 2607 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2534 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2476 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 2473 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 2407 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L31 · Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound… · 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 D against A, TM-score 0.91
- 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 0.89
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 7L31 · PDBe 7L31 · UniProt P23416 · UniProt P48167
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