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Iodowillardiine bound to a double cysteine mutant (A452C/S652C) of the ligand binding domain of GLUA2
Analyse Iodowillardiine bound to a double cysteine mutant (A452C/S652C) of the ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T96
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- IWD, ZN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- IWD · 2-amino-3-(5-iodo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-propionic acid · ligand · 3 copies · chains B, D, F
- ZN · Zinc ion · metal · 5 copies · chains B, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.82 | 0.85 | 117 | empty |
| 2 | 62 | 0.71 | 0.97 | 20 | IWD |
| 3 | 64 | 0.71 | 0.97 | 21 | IWD |
| 4 | 61 | 0.71 | 0.97 | 18 | IWD |
| 5 | 283 | 0.62 | 0.80 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–D · 937 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 284 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3T96 · Iodowillardiine bound to a double cysteine mutant (A452C/S652C) of the ligand binding… · the same entry in another collection · chain B against B, 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 P19491
- Elsewhere: RCSB PDB 3T96 · PDBe 3T96 · UniProt P19491
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