MolNFT v1 · #115522 · protein
Mnemiopsis leidyi ML032222A iglur lbd E423S mutant glycine complex
5CMC: “Mnemiopsis leidyi ML032222A iglur lbd E423S mutant glycine complex”. X-ray diffraction, 3 ligands (GLY, MG, SO4), 7 pockets (best druggability 0.61). MolNFT v1 #115522 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CMC
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ML032222A iglur
- Ligands
- GLY, MG, SO4
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ML032222A iglur | protein | 247 | 36% helix, 28% strand | — |
| B | ML032222A iglur | protein | 255 | 35% helix, 25% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.61 | 0.81 | 33 | empty |
| 2 | 135 | 0.55 | 0.82 | 23 | empty |
| 3 | 131 | 0.53 | 0.81 | 21 | empty |
| 4 | 113 | 0.41 | 0.76 | 23 | empty |
| 5 | 97 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1013 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5CMC · Mnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex · 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
- Elsewhere: RCSB PDB 5CMC · PDBe 5CMC
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