Research workbench
Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 ångströms (R3)
Analyse Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I5D
- Type
- protein
- Length
- 977 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2X purinoceptor
- UniProt
- Q6NYR1
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P2X purinoceptor | protein | 324 | 18% helix, 39% strand | Q6NYR1 |
| B | P2X purinoceptor | protein | 328 | 20% helix, 36% strand | Q6NYR1 |
| C | P2X purinoceptor | protein | 325 | 19% helix, 38% strand | Q6NYR1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.87 | 0.91 | 48 | empty |
| 2 | 992 | 0.81 | 0.82 | 60 | empty |
| 3 | 722 | 0.75 | 0.80 | 85 | empty |
| 4 | 601 | 0.73 | 0.80 | 75 | empty |
| 5 | 116 | 0.73 | 0.93 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1832 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1772 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1729 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 3I5D · Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5… · 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 Q6NYR1
- Elsewhere: RCSB PDB 3I5D · PDBe 3I5D · UniProt Q6NYR1
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