MolNFT v1 · #165535 · protein
Crystal structure of mammalian ric-8A:GALPHA(I):NANOBODY complex
6TYL · Resistance to inhibitors of cholinesterase 8 homolog a (C.…: “Crystal structure of mammalian ric-8A:GALPHA(I):NANOBODY complex”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #165535 on GenesisL1: 3D structure…
- PDB
- 6TYL
- Type
- protein
- Length
- 2,021 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Resistance to inhibitors of cholinesterase 8 homolog a (C. elegans); Nanobody a; Nanobody…
- UniProt
- B1H241, P10824
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Resistance to inhibitors of cholinesterase 8 homolog a (C. elegans) | protein | 484 | 58% helix, 2% strand | B1H241 |
| C | Nanobody a | protein | 112 | 0% helix, 43% strand | — |
| H | Nanobody a | protein | 111 | 0% helix, 48% strand | — |
| E | Nanobody B | protein | 106 | 0% helix, 39% strand | — |
| J | Nanobody B | protein | 113 | 3% helix, 34% strand | — |
| D, I | Nanobody C | protein | 121 | 5% helix, 46% strand | — |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 190 | 31% helix, 12% strand | P10824 |
| G | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 187 | 30% helix, 10% strand | P10824 |
| F | Resistance to inhibitors of cholinesterase 8 homolog a (C. elegans) | protein | 476 | 57% helix, 2% strand | B1H241 |
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 | 1105 | 0.85 | 0.86 | 101 | empty |
| 2 | 1170 | 0.84 | 0.85 | 97 | empty |
| 3 | 751 | 0.79 | 0.83 | 66 | empty |
| 4 | 818 | 0.79 | 0.82 | 81 | empty |
| 5 | 103 | 0.77 | 0.97 | 23 | empty |
Interfaces
17 interfaces between chains.
- A–B · 3371 Ų buried · 29 hydrogen bonds · protein-protein
- G–F · 3054 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1083 Ų buried · 13 hydrogen bonds · protein-protein
- H–F · 1008 Ų buried · 9 hydrogen bonds · protein-protein
- I–F · 995 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 modified (disulfide, phosphorylation).
Compared structures
- 6TYL · Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex · the same entry in another collection · chain F against F, TM-score 1.00
- P10824 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.72
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 B1H241
- Every structure of UniProt P10824
- Elsewhere: RCSB PDB 6TYL · PDBe 6TYL · UniProt B1H241 · UniProt P10824
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