MolNFT v1 · #168475 · protein
GLUN1B-GLUN2B NMDA receptor in non-active 1 conformation at 3.95 ångström resolution
6WHS · Glutamate receptor ionotropic, NMDA 1: “GLUN1B-GLUN2B NMDA receptor in non-active 1 conformation at 3.95 ångström resolution”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #168475 on GenesisL1…
- PDB
- 6WHS
- Type
- protein
- Length
- 3,172 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 799 | 37% helix, 17% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 787 | 36% helix, 15% strand | Q00960 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D, A, C
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 | 1090 | 0.84 | 0.85 | 126 | empty |
| 2 | 796 | 0.82 | 0.85 | 118 | empty |
| 3 | 1196 | 0.80 | 0.81 | 155 | empty |
| 4 | 1021 | 0.78 | 0.80 | 106 | empty |
| 5 | 947 | 0.78 | 0.80 | 105 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3015 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 2991 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 2832 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2817 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6WHS · GluN1b-GluN2B NMDA receptor in non-active 1 conformation at 3.95 angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P35439
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 6WHS · PDBe 6WHS · UniProt P35439 · UniProt Q00960
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.