MolNFT v1 · #106664 · protein
Crystal structure of GLUN1/GLUN2B NMDA receptor, structure 2
4TLM · Receptor subunit GLUN1: “Crystal structure of GLUN1/GLUN2B NMDA receptor, structure 2”. X-ray diffraction, 4 ligands (QEM, 1AC, JEG), 20 pockets (best druggability 0.86). MolNFT v1 #106664 on GenesisL1: 3D structure, binding sites…
- PDB
- 4TLM
- Type
- protein
- Length
- 3,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor subunit GLUN1; Receptor subunit GLUN2B
- UniProt
- C0KD18, A7XY94
- Ligands
- QEM, 1AC, JEG, NAG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor subunit GLUN1 | protein | 796 | 41% helix, 17% strand | C0KD18 |
| B | Receptor subunit GLUN2B | protein | 749 | 38% helix, 17% strand | A7XY94 |
| C | Receptor subunit GLUN1 | protein | 750 | 41% helix, 16% strand | C0KD18 |
| D | Receptor subunit GLUN2B | protein | 753 | 39% helix, 17% strand | A7XY94 |
Ligands and binding sites
- QEM · 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol · ligand · 2 copies · chains A, B, C, D
- 1AC · 1-aminocyclopropanecarboxylic acid · ligand · chains A
- JEG · trans-1-aminocyclobutane-1,3-dicarboxylic acid · ligand · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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 | 820 | 0.86 | 0.88 | 132 | empty |
| 2 | 765 | 0.84 | 0.87 | 105 | empty |
| 3 | 725 | 0.83 | 0.86 | 124 | empty |
| 4 | 1020 | 0.81 | 0.82 | 106 | empty |
| 5 | 801 | 0.81 | 0.84 | 99 | QEM |
Interfaces
6 interfaces between chains.
- A–B · 2191 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2024 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1659 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1458 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 273 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4TLM · Crystal structure of GluN1/GluN2B NMDA receptor, structure 2 · the same entry in another collection · chain A against A, TM-score 1.00
- A7XY94 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (A7XY94) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 C0KD18
- Every structure of UniProt A7XY94
- Elsewhere: RCSB PDB 4TLM · PDBe 4TLM · UniProt C0KD18 · UniProt A7XY94
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