MolNFT v1 · #180866 · protein
Native AMPA receptor
7LDE · Glutamate receptor 1: “Native AMPA receptor”. Electron microscopy, 8 ligands (D10, D12, C14), 20 pockets (best druggability 0.83). MolNFT v1 #180866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LDE
- Type
- protein
- Length
- 4,990 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 1; Glutamate receptor; Protein cornichon homolog 2; Voltage-dependent…
- UniProt
- P23818, G5E8H1, O35089, Q8VHW2
- Ligands
- D10, D12, C14, ZK1, HP6, R16, XVD, NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 1 | protein | 776 | 41% helix, 17% strand | P23818 |
| B, D | Glutamate receptor | protein | 778 | 41% helix, 14% strand | G5E8H1 |
| E, F | Protein cornichon homolog 2 | protein | 124 | 86% helix, 0% strand | O35089 |
| G, H | Voltage-dependent calcium channel gamma-8 subunit | protein | 162 | 62% helix, 7% strand | Q8VHW2 |
| I, L | 11B8 scfv | protein | 229 | 1% helix, 34% strand | — |
| J, M | 15F1 Fab light chain | protein | 211 | 6% helix, 40% strand | — |
| K, N | 15F1 Fab heavy chain | protein | 215 | 2% helix, 32% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 6 copies · chains A, D, B, C, E, F
- D12 · Dodecane · ligand · 6 copies · chains B, C, A, D, G, H
- C14 · Tetradecane · ligand · 6 copies · chains A, B, C, D, G, H
- ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
- HP6 · Heptane · ligand · 4 copies · chains A, G, B, C, H
- R16 · Hexadecane · ligand · 2 copies · chains A, C
- XVD · 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol · ligand · 2 copies · chains A, G, C, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C, D
- OCT · N-octane · additive · 6 copies · chains A, B, F, C, D, E, G, H
- DD9 · nonane · additive · 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 | 1041 | 0.83 | 0.84 | 124 | empty |
| 2 | 1105 | 0.83 | 0.84 | 133 | empty |
| 3 | 1107 | 0.83 | 0.84 | 104 | empty |
| 4 | 1107 | 0.81 | 0.83 | 107 | empty |
| 5 | 794 | 0.80 | 0.83 | 93 | empty |
Interfaces
22 interfaces between chains.
- C–D · 3549 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 3476 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 3287 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 3280 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 770 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LDE · native AMPA receptor · the same entry in another collection · chain N against N, 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 P23818
- Every structure of UniProt G5E8H1
- Every structure of UniProt O35089
- Every structure of UniProt Q8VHW2
- Elsewhere: RCSB PDB 7LDE · PDBe 7LDE · UniProt P23818 · UniProt G5E8H1 · UniProt O35089 · UniProt Q8VHW2
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