Research workbench
Cryo-EM structure of GLUN1B-2B nmdar in complex with FAB5 in non- ACTIVE1 conformation
Analyse Cryo-EM structure of GLUN1B-2B nmdar in complex with FAB5 in non- ACTIVE1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TES
- Type
- protein
- Length
- 3,986 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B; FAB5 heavy…
- UniProt
- P35439, Q00960
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 789 | 36% helix, 13% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 774 | 36% helix, 15% strand | Q00960 |
| H, M | FAB5 heavy chain | protein | 215 | 1% helix, 41% strand | — |
| L, N | FAB5 light chain | protein | 215 | 4% helix, 42% strand | — |
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 | 1148 | 0.88 | 0.89 | 131 | empty |
| 2 | 264 | 0.84 | 0.95 | 49 | empty |
| 3 | 981 | 0.83 | 0.84 | 115 | empty |
| 4 | 609 | 0.83 | 0.87 | 60 | empty |
| 5 | 221 | 0.83 | 0.95 | 31 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3184 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 3170 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 3012 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2905 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1885 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7TES · Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 in Non-active1 conformation · the same entry in another collection · chain A against A, TM-score 1.00
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 7TES · PDBe 7TES · UniProt P35439 · UniProt Q00960
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