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Structure of full-length IP3R1 channel solubilized in lnmg & lipid in the apo-state
Analyse Structure of full-length IP3R1 channel solubilized in lnmg & lipid in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LHF
- Type
- protein
- Length
- 9,200 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 0.85
Structure
electron microscopy · 1 distinct chain · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Inositol 1,4,5-trisphosphate receptor type 1 | protein | 2300 | 45% 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, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.85 | 0.85 | 68 | empty |
| 2 | 901 | 0.83 | 0.84 | 100 | empty |
| 3 | 880 | 0.83 | 0.84 | 100 | empty |
| 4 | 833 | 0.83 | 0.85 | 88 | empty |
| 5 | 1101 | 0.82 | 0.82 | 108 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4369 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 4361 Ų buried · 28 hydrogen bonds · protein-protein
- D–C · 4361 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 4360 Ų buried · 26 hydrogen bonds · protein-protein
- D–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 covalent (covalent ligand).
Compared structures
- 7LHF · Structure of full-length IP3R1 channel solubilized in LNMG & lipid 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 7LHF · PDBe 7LHF · UniProt P29994
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