MolNFT v1 · #158087 · protein
Architecture and subunit arrangement of native AMPA receptors
6NJM · Glutamate receptor 3: “Architecture and subunit arrangement of native AMPA receptors”. Electron microscopy, 3 ligands (ZK1, NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #158087 on GenesisL1: 3D structure, binding sites…
- PDB
- 6NJM
- Type
- protein
- Length
- 5,420 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 3; Glutamate receptor 2; A'-C' auxiliary proteins; Voltage-dependent…
- UniProt
- P19492, P19491, Q71RJ2
- Ligands
- ZK1, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 3 | protein | 784 | 43% helix, 17% strand | P19492 |
| B, D | Glutamate receptor 2 | protein | 783 | 41% helix, 17% strand | P19491 |
| E, G | A'-C' auxiliary proteins | protein | 117 | 93% helix, 0% strand | — |
| F, H | Voltage-dependent calcium channel gamma-2 subunit | protein | 169 | 69% helix, 9% strand | Q71RJ2 |
| I, M | 5B2 Fab light chain | protein | 218 | 1% helix, 51% strand | — |
| J, N | 5B2 Fab heavy chain | protein | 213 | 7% helix, 54% strand | — |
| K, O | 15F1 Fab light chain | protein | 211 | 5% helix, 48% strand | — |
| L, P | 15F1 Fab heavy chain | protein | 215 | 1% helix, 52% strand | — |
Ligands and binding sites
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
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 | 848 | 0.86 | 0.88 | 117 | ZK1 |
| 2 | 990 | 0.83 | 0.84 | 102 | ZK1 |
| 3 | 834 | 0.83 | 0.85 | 94 | empty |
| 4 | 488 | 0.82 | 0.88 | 66 | empty |
| 5 | 1192 | 0.81 | 0.82 | 143 | empty |
Interfaces
28 interfaces between chains.
- A–B · 3483 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3452 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2815 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2757 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 733 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 10 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6NJM · Architecture and subunit arrangement of native AMPA receptors · the same entry in another collection · chain P against P, 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 P19492
- Every structure of UniProt P19491
- Every structure of UniProt Q71RJ2
- Elsewhere: RCSB PDB 6NJM · PDBe 6NJM · UniProt P19492 · UniProt P19491 · UniProt Q71RJ2
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