MolNFT v1 · #177032 · protein
Crystal structure of GDP-bound gnas in complex with the cyclic peptide inhibitor GD20
7E5E · Isoform gnas-2 of guanine nucleotide-binding protein G(S)…: “Crystal structure of GDP-bound gnas in complex with the cyclic peptide inhibitor GD20”. X-ray diffraction, 4 ligands (ACE, GDP, NH2), 19 pockets (best druggability 0.84).…
- PDB
- 7E5E
- Type
- protein
- Length
- 1,371 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short…
- UniProt
- P63092
- Ligands
- ACE, GDP, NH2, CL
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 338 | 50% helix, 15% strand | P63092 |
| B | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 324 | 51% helix, 14% strand | P63092 |
| C | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 332 | 50% helix, 15% strand | P63092 |
| D | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 317 | 50% helix, 15% strand | P63092 |
| E, F, G, H | GD20 | protein | 15 | 33% helix, 7% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains B, E, A, F, D, G, C, H
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NH2 · Amino group · ion · 4 copies · chains E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.84 | 0.89 | 79 | GDP |
| 2 | 559 | 0.84 | 0.89 | 75 | ACE, GDP, CL |
| 3 | 630 | 0.84 | 0.88 | 81 | GDP |
| 4 | 464 | 0.83 | 0.91 | 61 | ACE, GDP, CL |
| 5 | 984 | 0.76 | 0.78 | 77 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1020 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 726 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 722 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 721 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 d-amino (covalent ligand, D-amino acid).
Compared structures
- 7E5E · Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20 · the same entry in another collection · chain H against H, TM-score 1.00
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 P63092
- Elsewhere: RCSB PDB 7E5E · PDBe 7E5E · UniProt P63092
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