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Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state
Analyse Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LHE
- Type
- protein
- Length
- 9,192 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol 1,4,5-trisphosphate receptor type 1
- UniProt
- P29994
- Ligands
- PLX, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, B | Inositol 1,4,5-trisphosphate receptor type 1 | protein | 2298 | 47% helix, 6% strand | P29994 |
Ligands and binding sites
- PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · 28 copies · chains A, B, D, C
- ZN · Zinc ion · metal · 4 copies · chains A, D, C, B
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 | 952 | 0.86 | 0.88 | 65 | empty |
| 2 | 1099 | 0.85 | 0.86 | 142 | empty |
| 3 | 1055 | 0.84 | 0.84 | 50 | empty |
| 4 | 1147 | 0.80 | 0.81 | 108 | empty |
| 5 | 1130 | 0.80 | 0.81 | 114 | empty |
Interfaces
6 interfaces between chains.
- C–B · 4378 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 4377 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 4373 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 4372 Ų buried · 22 hydrogen bonds · protein-protein
- D–B · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LHE · Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state · 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 P29994
- Elsewhere: RCSB PDB 7LHE · PDBe 7LHE · UniProt P29994
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