Research workbench
IP3, ATP, and CA2+ bound type 3 IP3 receptor in the inactive state
Analyse IP3, ATP, and CA2+ bound type 3 IP3 receptor in the inactive state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T3U
- Type
- protein
- Length
- 7,269 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol 1,4,5-trisphosphate receptor type 3
- UniProt
- Q14573
- Ligands
- ATP, I3P, ZN, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inositol 1,4,5-trisphosphate receptor type 3 | protein | 2020 | 57% helix, 8% strand | Q14573 |
| B | Inositol 1,4,5-trisphosphate receptor type 3 | protein | 1662 | 69% helix, 1% strand | Q14573 |
| C | Inositol 1,4,5-trisphosphate receptor type 3 | protein | 1575 | 67% helix, 2% strand | Q14573 |
| D | Inositol 1,4,5-trisphosphate receptor type 3 | protein | 2012 | 59% helix, 8% strand | Q14573 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 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 | 968 | 0.85 | 0.86 | 67 | empty |
| 2 | 731 | 0.84 | 0.88 | 97 | empty |
| 3 | 1040 | 0.84 | 0.85 | 119 | empty |
| 4 | 1013 | 0.83 | 0.84 | 133 | empty |
| 5 | 1102 | 0.82 | 0.84 | 164 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2505 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2503 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2297 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2230 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7T3U · IP3, ATP, and Ca2+ bound type 3 IP3 receptor in the inactive state · the same entry in another collection · chain A against A, TM-score 1.00
- Q14573 · AlphaFold monomer V2.0 prediction for inositol 1,4,5-trisphosphate receptor type 3… · a predicted model of the same protein · chain B against A, TM-score 0.74
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 Q14573
- Elsewhere: RCSB PDB 7T3U · PDBe 7T3U · UniProt Q14573
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