MolNFT v1 · #190703 · protein
Cryo-EM structure of mrgd-gi complex with beta-alanine
7Y12 · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of mrgd-gi complex with beta-alanine”. Electron microscopy, 2 ligands (PLM, BAL), 9 pockets (best druggability 0.81). MolNFT v1 #190703 on GenesisL1: 3D…
- PDB
- 7Y12
- Type
- protein
- Length
- 1,109 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62874, P63213, Q8TDS7
- Ligands
- PLM, BAL
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 46% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 43% strand | P62874 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 49% helix, 0% strand | P63213 |
| R | Soluble cytochrome B562,MAS-related G-protein coupled receptor member D | protein | 264 | 80% helix, 0% strand | Q8TDS7 |
| S | SCFV16 | protein | 232 | 3% helix, 46% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.81 | 0.85 | 62 | empty |
| 2 | 862 | 0.74 | 0.79 | 69 | empty |
| 3 | 388 | 0.67 | 0.80 | 65 | empty |
| 4 | 193 | 0.55 | 0.78 | 24 | PLM |
| 5 | 74 | 0.54 | 0.86 | 26 | BAL |
Interfaces
6 interfaces between chains.
- B–C · 2146 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 1211 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1076 Ų buried · 13 hydrogen bonds · protein-protein
- A–S · 576 Ų buried · 7 hydrogen bonds · protein-protein
- B–S · 430 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7Y12 · Cryo-EM structure of MrgD-Gi complex with beta-alanine · the same entry in another collection · chain S against S, TM-score 1.00
- P62874 · 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
- Q8TDS7 · AlphaFold monomer V2.0 prediction for mas-related G-protein coupled receptor member D… · a predicted model of the same protein · chain R against A, TM-score 0.92
- P63213 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C 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 0.80
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 P62874
- Every structure of UniProt P63213
- Every structure of UniProt Q8TDS7
- Elsewhere: RCSB PDB 7Y12 · PDBe 7Y12 · UniProt P63096 · UniProt P62874 · UniProt P63213 · UniProt Q8TDS7
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