Research workbench
Cryo-EM reveals partially and fully assembled native glycine RECEPTORS,HOMOMERIC pentamer
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
- 7MLU
- Type
- protein
- Length
- 2,746 residues
- Chains
- 15
- 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
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, O | 3D1 Fab light chain | protein | 102 | 3% helix, 28% strand | — |
| F, G, N, L, H | 3D1 Fab heavy chain | protein | 115 | 3% helix, 38% strand | — |
| J | 3D1 Fab light chain | protein | 101 | 0% helix, 31% strand | — |
| M, I | 3D1 Fab light chain | protein | 103 | 3% helix, 41% strand | — |
| A, E, D, B, C | Glycine receptor alpha 1 | protein | 332 | 31% helix, 24% strand | F1RQB7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, E, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.85 | 0.85 | 122 | empty |
| 2 | 1094 | 0.80 | 0.81 | 120 | empty |
| 3 | 1145 | 0.79 | 0.81 | 126 | empty |
| 4 | 1167 | 0.79 | 0.81 | 125 | empty |
| 5 | 733 | 0.79 | 0.83 | 63 | empty |
Interfaces
30 interfaces between chains.
- E–D · 2453 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2439 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2428 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2406 Ų buried · 21 hydrogen bonds · protein-protein
- D–C · 2405 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7MLU · Cryo-EM reveals partially and fully assembled native glycine receptors,homomeric pentamer · the same entry in another collection · chain K against K, 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 7MLU · PDBe 7MLU · UniProt F1RQB7
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