MolNFT v1 · #168476 · protein
GLUN1B-GLUN2B NMDA receptor in active conformation at 4.4 ångström resolution
6WHT · Glutamate receptor ionotropic, NMDA 1: “GLUN1B-GLUN2B NMDA receptor in active conformation at 4.4 ångström resolution”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v1 #168476 on GenesisL1: 3D…
- PDB
- 6WHT
- Type
- protein
- Length
- 3,082 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 0.89
Structure
electron microscopy · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 793 | 38% helix, 14% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 748 | 39% helix, 11% strand | Q00960 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, 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 | 1039 | 0.89 | 0.90 | 131 | empty |
| 2 | 969 | 0.83 | 0.84 | 134 | empty |
| 3 | 566 | 0.83 | 0.88 | 103 | empty |
| 4 | 1050 | 0.82 | 0.83 | 140 | empty |
| 5 | 425 | 0.82 | 0.90 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2068 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2054 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1985 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1961 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 151 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6WHT · GluN1b-GluN2B NMDA receptor in active conformation at 4.4 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 0.89
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 6WHT · PDBe 6WHT · UniProt P35439 · UniProt Q00960
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