MolNFT v1 · #152069 · protein
Crystal structure of the kdel receptor bound to synthetic nanobody.
6I6J · Er lumen protein-retaining receptor 2: “Crystal structure of the kdel receptor bound to synthetic nanobody.”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #152069 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6I6J
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Er lumen protein-retaining receptor 2; Sybody
- UniProt
- Q5ZKX9
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Er lumen protein-retaining receptor 2 | protein | 204 | 75% helix, 0% strand | Q5ZKX9 |
| C | Sybody | protein | 121 | 7% helix, 54% strand | — |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.78 | 0.95 | 31 | empty |
| 2 | 128 | 0.63 | 0.87 | 21 | empty |
| 3 | 63 | 0.63 | 0.93 | 18 | empty |
| 4 | 100 | 0.58 | 0.86 | 18 | OLC |
Interfaces
1 interface between chains.
- A–C · 1274 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6I6J · Crystal structure of the KDEL receptor bound to synthetic nanobody. · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZKX9 · AlphaFold monomer V2.0 prediction for er lumen protein-retaining receptor 2 (Q5ZKX9) · a predicted model of the same protein · chain A 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 Q5ZKX9
- Elsewhere: RCSB PDB 6I6J · PDBe 6I6J · UniProt Q5ZKX9
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