MolNFT v1 · #54480 · protein
Pentameric ligand gated ion channel glic in complex with cadmium ion (CD2+)
2XQ7 · GLR4197 protein: “Pentameric ligand gated ion channel glic in complex with cadmium ion (CD2+)”. X-ray diffraction, 1 ligand (CD), 20 pockets (best druggability 0.80). MolNFT v1 #54480 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XQ7
- Type
- protein
- Length
- 1,550 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLR4197 protein
- UniProt
- Q7NDN8
- Ligands
- CD
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | GLR4197 protein | protein | 310 | 33% helix, 30% strand | Q7NDN8 |
Ligands and binding sites
- CD · Cadmium ion · metal · 5 copies · chains A, C, D, E, 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 | 1089 | 0.80 | 0.81 | 58 | CD |
| 2 | 539 | 0.70 | 0.80 | 67 | empty |
| 3 | 75 | 0.69 | 0.95 | 19 | empty |
| 4 | 65 | 0.69 | 0.95 | 18 | empty |
| 5 | 65 | 0.69 | 0.95 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2322 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2265 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2241 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2143 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 2137 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2XQ7 · Pentameric ligand gated ion channel GLIC in complex with cadmium ion (Cd2+) · the same entry in another collection · chain E against E, TM-score 1.00
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q7NDN8
- Elsewhere: RCSB PDB 2XQ7 · PDBe 2XQ7 · UniProt Q7NDN8
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