Research workbench
Heterotrimeric G-protein in complex with an antibody fragment
Analyse Heterotrimeric G-protein in complex with an antibody fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRK
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768
- Ligands
- GDP
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 345 | 53% helix, 13% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 60 | 70% helix, 0% strand | P59768 |
| H | Single-chain fv | protein | 236 | 4% helix, 48% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.82 | 0.85 | 67 | empty |
| 2 | 460 | 0.70 | 0.81 | 55 | GDP |
| 3 | 311 | 0.59 | 0.77 | 48 | empty |
| 4 | 204 | 0.57 | 0.80 | 28 | empty |
| 5 | 319 | 0.56 | 0.76 | 46 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2238 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1290 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 579 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 443 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 44 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6CRK · Heterotrimeric G-protein in complex with an antibody fragment · the same entry in another collection · chain A against A, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.92
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6CRK · PDBe 6CRK · UniProt P63096 · UniProt P62873 · UniProt P59768
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