Research workbench
Structure of the human GLUN1/GLUN2A NMDA receptor in the GLUTAMATE/GLYCINE-bound state at pH 6.3, class III
Analyse Structure of the human GLUN1/GLUN2A NMDA receptor in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IRH
- Type
- protein
- Length
- 3,083 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2A
- UniProt
- Q05586, Q12879
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 786 | 38% helix, 17% strand | Q05586 |
| D, B | Glutamate receptor ionotropic, NMDA 2A | protein | 756 | 36% helix, 13% strand | Q12879 |
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 785 | 38% helix, 17% strand | Q05586 |
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 | 952 | 0.87 | 0.89 | 116 | empty |
| 2 | 1031 | 0.87 | 0.88 | 110 | empty |
| 3 | 1122 | 0.86 | 0.87 | 117 | empty |
| 4 | 214 | 0.82 | 0.95 | 38 | empty |
| 5 | 209 | 0.82 | 0.95 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3187 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3180 Ų buried · 35 hydrogen bonds · protein-protein
- C–B · 2295 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 2288 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 202 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6IRH · Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at… · the same entry in another collection · chain C against C, TM-score 1.00
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · 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 Q05586
- Every structure of UniProt Q12879
- Elsewhere: RCSB PDB 6IRH · PDBe 6IRH · UniProt Q05586 · UniProt Q12879
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