MolNFT v1 · #168478 · protein
GLUN1B-GLUN2B NMDA receptor in complex with sdz 220-040 and L689,560, class 2
6WHV · Glutamate receptor ionotropic, NMDA 1: “GLUN1B-GLUN2B NMDA receptor in complex with sdz 220-040 and L689,560, class 2”. Electron microscopy, 3 ligands (QGP, QGM, NAG), 20 pockets (best druggability 0.85). MolNFT v1 #168478 on…
- PDB
- 6WHV
- Type
- protein
- Length
- 3,170 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
- QGP, QGM, NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 803 | 34% helix, 16% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 783 | 34% helix, 9% strand | Q00960 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 800 | 36% helix, 14% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 784 | 35% helix, 13% strand | Q00960 |
Ligands and binding sites
- QGP · (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid · ligand · 2 copies · chains B, D
- QGM · (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A, 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 | 1178 | 0.85 | 0.86 | 137 | QGM |
| 2 | 605 | 0.83 | 0.88 | 104 | empty |
| 3 | 552 | 0.82 | 0.88 | 60 | empty |
| 4 | 1189 | 0.82 | 0.83 | 132 | empty |
| 5 | 1157 | 0.81 | 0.82 | 125 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3373 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 3147 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3086 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 3059 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 5 covalent, 5 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6WHV · GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 2 · the same entry in another collection · chain D against D, TM-score 1.00
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.92
- 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 6WHV · PDBe 6WHV · UniProt P35439 · UniProt Q00960
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