Research workbench
Gppnhp-bound YPT51 at 1.48 a resolution
Analyse Gppnhp-bound YPT51 at 1.48 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EK0
- Type
- protein
- Length
- 170 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (GTP-binding protein YPT51)
- UniProt
- P36017
- Ligands
- GNP, GDP, MG, NI
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (GTP-binding protein YPT51) | protein | 170 | 37% helix, 27% strand | P36017 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.54 | 0.80 | 27 | MG, GNP |
| 2 | 52 | 0.39 | 0.81 | 18 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
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 P36017
- Elsewhere: RCSB PDB 1EK0 · PDBe 1EK0 · UniProt P36017
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