MolNFT v1 · #136314 · protein
Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2B in complex with glycine, glutamate, ro 25-6981, mk-801 and a GLUN2B-specific Fab, at pH 6.5
5UP2 · N-methyl-D-aspartate receptor subunit NR1-8A: “Triheteromeric NMDA receptor GLUN1/GLUN2A/GLUN2B in complex with glycine, glutamate, ro 25-6981, mk-801 and a…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability…
- PDB
- 5UP2
- Type
- protein
- Length
- 3,612 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-methyl-D-aspartate receptor subunit NR1-8A; N-methyl-D-aspartate receptor subunit NR2A…
- UniProt
- C0KD18, B7ZSK1, A7XY94
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 6 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-methyl-D-aspartate receptor subunit NR1-8A | protein | 796 | 40% helix, 15% strand | C0KD18 |
| B | N-methyl-D-aspartate receptor subunit NR2A | protein | 795 | 40% helix, 14% strand | B7ZSK1 |
| C | N-methyl-D-aspartate receptor subunit NR1-8A | protein | 798 | 40% helix, 16% strand | C0KD18 |
| D | Ionotropic glutamate receptor subunit NR2B | protein | 794 | 40% helix, 16% strand | A7XY94 |
| F | GLUN2B-specific Fab, termed 11D1 | protein | 214 | 6% helix, 53% strand | — |
| G | GLUN2B-specific Fab, termed 11D1 | protein | 215 | 7% helix, 56% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, 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 | 1187 | 0.89 | 0.90 | 148 | empty |
| 2 | 1043 | 0.89 | 0.90 | 136 | empty |
| 3 | 1062 | 0.88 | 0.90 | 174 | empty |
| 4 | 1030 | 0.87 | 0.88 | 124 | empty |
| 5 | 1183 | 0.86 | 0.87 | 177 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3197 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1816 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 1805 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1499 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 795 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5UP2 · Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro… · the same entry in another collection · chain G against G, TM-score 1.00
- B7ZSK1 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (B7ZSK1) · a predicted model of the same protein · chain B against A, TM-score 0.93
- 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 0.92
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 C0KD18
- Every structure of UniProt B7ZSK1
- Every structure of UniProt A7XY94
- Elsewhere: RCSB PDB 5UP2 · PDBe 5UP2 · UniProt C0KD18 · UniProt B7ZSK1 · UniProt A7XY94
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