Research workbench
Crystal structure of YPT7 covalently modified with GDP
Analyse Crystal structure of YPT7 covalently modified with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHF
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein YPT7
- UniProt
- P32939
- Ligands
- 2UH, MG, NO3
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein YPT7 | protein | 163 | 37% helix, 27% strand | P32939 |
Ligands and binding sites
- 2UH · N-[3-(propanoylamino)propyl]guanosine 5'-(trihydrogen diphosphate) · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.29 | 0.75 | 15 | NO3 |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 P32939
- Elsewhere: RCSB PDB 4PHF · PDBe 4PHF · UniProt P32939
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