MolNFT v1 · #158086 · protein
Architecture and subunit arrangement of native AMPA receptors
6NJL · Glutamate receptor 1: “Architecture and subunit arrangement of native AMPA receptors”. Electron microscopy, 2 ligands (ZK1, NAG), 20 pockets (best druggability 0.83). MolNFT v1 #158086 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NJL
- Type
- protein
- Length
- 5,018 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 1; Glutamate receptor 2; A'/C' auxiliary proteins; Voltage-dependent…
- UniProt
- P19490, P19491, Q71RJ2
- Ligands
- ZK1, NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 1 | protein | 785 | 43% helix, 17% strand | P19490 |
| B, D | Glutamate receptor 2 | protein | 783 | 40% helix, 18% 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, L | 11B8 scfv | protein | 229 | 1% helix, 47% strand | — |
| J, M | 15F1 Fab light chain | protein | 211 | 5% helix, 50% strand | — |
| K, N | 15F1 Fab heavy chain | protein | 215 | 0% 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 · 18 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 | 794 | 0.83 | 0.86 | 90 | empty |
| 2 | 644 | 0.82 | 0.87 | 82 | ZK1 |
| 3 | 1093 | 0.82 | 0.83 | 108 | empty |
| 4 | 1064 | 0.82 | 0.83 | 122 | ZK1 |
| 5 | 494 | 0.82 | 0.88 | 78 | empty |
Interfaces
22 interfaces between chains.
- C–D · 3471 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 3455 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2746 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 2734 Ų buried · 9 hydrogen bonds · protein-protein
- C–H · 642 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NJL · Architecture and subunit arrangement of native AMPA receptors · 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 P19490
- Every structure of UniProt P19491
- Every structure of UniProt Q71RJ2
- Elsewhere: RCSB PDB 6NJL · PDBe 6NJL · UniProt P19490 · UniProt P19491 · UniProt Q71RJ2
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