Research workbench
Structure of the apo human GLUN1/GLUN2A lbd
Analyse Structure of the apo human GLUN1/GLUN2A lbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H8F
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
- UniProt
- Q12879, Q05586
- Ligands
- GLU, GLY
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 2A | protein | 274 | 33% helix, 26% strand | Q12879 |
| B | Glutamate receptor ionotropic, NMDA 1 | protein | 283 | 31% helix, 27% strand | Q05586 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- GLY · Glycine · ligand · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.78 | 0.82 | 88 | GOL |
| 2 | 193 | 0.58 | 0.81 | 29 | empty |
| 3 | 60 | 0.58 | 0.91 | 20 | GLU |
| 4 | 77 | 0.55 | 0.87 | 24 | empty |
| 5 | 77 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1241 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5H8F · Structure of the apo human GluN1/GluN2A LBD · the same entry in another collection · chain B against B, TM-score 1.00
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q12879
- Every structure of UniProt Q05586
- Elsewhere: RCSB PDB 5H8F · PDBe 5H8F · UniProt Q12879 · UniProt Q05586
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