MolNFT v1 · #36995 · protein
An open conformation of switch I revealed by SAR1-GDP crystal structure at low MG(2+)
2FMX · GTP-binding protein SAR1B: “An open conformation of switch I revealed by SAR1-GDP crystal structure at low MG(2+)”. X-ray diffraction, 3 ligands (GDP, MG, SO4), 5 pockets (best druggability 0.58). MolNFT v1 #36995 on GenesisL1: 3D…
- PDB
- 2FMX
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein SAR1B
- UniProt
- Q9QVY3
- Ligands
- GDP, MG, SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein SAR1B | protein | 180 | 32% helix, 23% strand | Q9QVY3 |
| B | GTP-binding protein SAR1B | protein | 172 | 33% helix, 23% strand | Q9QVY3 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.58 | 0.79 | 36 | GDP |
| 2 | 183 | 0.46 | 0.75 | 32 | MG |
| 3 | 80 | 0.42 | 0.80 | 18 | empty |
| 4 | 54 | 0.29 | 0.75 | 15 | empty |
| 5 | 57 | 0.26 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2FMX · An open conformation of switch I revealed by Sar1-GDP crystal structure at low Mg(2+) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QVY3 · AlphaFold monomer V2.0 prediction for GTP-binding protein SAR1B (Q9QVY3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9QVY3
- Elsewhere: RCSB PDB 2FMX · PDBe 2FMX · UniProt Q9QVY3
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