Research workbench
Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mm calcium
Analyse Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mm calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MBQ
- Type
- protein
- Length
- 3,984 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential melastatin 5
- UniProt
- S5UH55
- Ligands
- YUV, YUY, NAG, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential melastatin 5 | protein | 996 | 62% helix, 8% strand | S5UH55 |
Ligands and binding sites
- YUV · (25R)-14beta,17beta-spirost-5-en-3beta-ol · ligand · 4 copies · chains A, B, C, D
- YUY · (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
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 | 1082 | 0.85 | 0.85 | 62 | empty |
| 2 | 94 | 0.75 | 0.96 | 24 | empty |
| 3 | 90 | 0.74 | 0.96 | 23 | empty |
| 4 | 91 | 0.74 | 0.96 | 24 | empty |
| 5 | 998 | 0.74 | 0.77 | 71 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3137 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 3136 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 3132 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 3130 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7MBQ · Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mM calcium · the same entry in another collection · chain A against A, 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 S5UH55
- Elsewhere: RCSB PDB 7MBQ · PDBe 7MBQ · UniProt S5UH55
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