MolNFT v1 · #154983 · protein
Rat GLUD1 RECEPTOR(COMPACT conformation) in complex with 7-cka and calcium ions
6KSS · Glutamate receptor ionotropic, delta-1: “Rat GLUD1 RECEPTOR(COMPACT conformation) in complex with 7-cka and calcium ions”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #154983 on GenesisL1: 3D structure…
- PDB
- 6KSS
- Type
- protein
- Length
- 3,012 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, delta-1
- UniProt
- Q62640
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor ionotropic, delta-1 | protein | 753 | 35% helix, 15% strand | Q62640 |
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 | 725 | 0.86 | 0.89 | 107 | empty |
| 2 | 974 | 0.85 | 0.86 | 121 | empty |
| 3 | 1021 | 0.84 | 0.85 | 122 | empty |
| 4 | 845 | 0.82 | 0.85 | 112 | empty |
| 5 | 979 | 0.82 | 0.83 | 105 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4257 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 4059 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 1088 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1014 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6KSS · Rat GluD1 receptor(compact conformation) in complex with 7-CKA and Calcium ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q62640 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, delta-1 (Q62640) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q62640
- Elsewhere: RCSB PDB 6KSS · PDBe 6KSS · UniProt Q62640
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