Research workbench
Cryo-EM reveals partially and fully assembled native glycine RECEPTORS,HOMOMERIC tetramer
Analyse Cryo-EM reveals partially and fully assembled native glycine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MLV
- Type
- protein
- Length
- 1,919 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D1 Fab light chain; 3D1 Fab heavy chain; Glycine receptor alpha 1
- UniProt
- F1RQB7
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 15% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | 3D1 Fab light chain | protein | 101 | 0% helix, 26% strand | — |
| G, F, L, H | 3D1 Fab heavy chain | protein | 115 | 0% helix, 37% strand | — |
| K | 3D1 Fab light chain | protein | 102 | 0% helix, 15% strand | — |
| M, I | 3D1 Fab light chain | protein | 103 | 0% helix, 36% strand | — |
| D | Glycine receptor alpha 1 | protein | 170 | 8% helix, 23% strand | F1RQB7 |
| A | Glycine receptor alpha 1 | protein | 310 | 22% helix, 18% strand | F1RQB7 |
| B | Glycine receptor alpha 1 | protein | 296 | 24% helix, 21% strand | F1RQB7 |
| C | Glycine receptor alpha 1 | protein | 274 | 23% helix, 20% strand | F1RQB7 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, I, C, D
- BMA · beta-D-mannopyranose · sugar · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.81 | 0.83 | 102 | empty |
| 2 | 1075 | 0.81 | 0.82 | 103 | empty |
| 3 | 801 | 0.81 | 0.84 | 95 | empty |
| 4 | 1040 | 0.81 | 0.82 | 99 | empty |
| 5 | 324 | 0.80 | 0.90 | 58 | empty |
Interfaces
21 interfaces between chains.
- B–C · 1844 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1688 Ų buried · 2 hydrogen bonds · protein-protein
- D–C · 878 Ų buried · 6 hydrogen bonds · protein-protein
- J–G · 852 Ų buried · 9 hydrogen bonds · protein-protein
- I–H · 836 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7MLV · Cryo-EM reveals partially and fully assembled native glycine receptors,homomeric tetramer · the same entry in another collection · chain J against J, TM-score 1.00
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 F1RQB7
- Elsewhere: RCSB PDB 7MLV · PDBe 7MLV · UniProt F1RQB7
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