Research workbench
Crystal structure of ampylated GRP78
Analyse Crystal structure of ampylated GRP78 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O4P
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein
- UniProt
- G3I8R9
- Ligands
- AMP, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 78 kda glucose-regulated protein | protein | 518 | 33% helix, 32% strand | G3I8R9 |
| B | 78 kda glucose-regulated protein | protein | 522 | 32% helix, 32% strand | G3I8R9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.71 | 0.84 | 45 | SO4 |
| 2 | 329 | 0.70 | 0.83 | 43 | SO4 |
| 3 | 556 | 0.62 | 0.75 | 59 | empty |
| 4 | 337 | 0.59 | 0.77 | 56 | empty |
| 5 | 278 | 0.53 | 0.75 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 9 hydrogen bonds · protein-protein
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 G3I8R9
- Elsewhere: RCSB PDB 5O4P · PDBe 5O4P · UniProt G3I8R9
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