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Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with 7-deaza-ADP and inorganic phosphate
Analyse Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EX5
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein
- UniProt
- P11021
- Ligands
- 7DD, MG, PO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 78 kda glucose-regulated protein | protein | 382 | 42% helix, 28% strand | P11021 |
| B | 78 kda glucose-regulated protein | protein | 379 | 41% helix, 28% strand | P11021 |
Ligands and binding sites
- 7DD · 7-deazaadenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.78 | 0.82 | 72 | MG, PO4, 7DD |
| 2 | 800 | 0.77 | 0.81 | 68 | MG, PO4, 7DD |
| 3 | 791 | 0.73 | 0.78 | 62 | empty |
| 4 | 89 | 0.44 | 0.80 | 14 | empty |
| 5 | 57 | 0.40 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 330 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EX5 · Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P11021 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P11021) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P11021
- Elsewhere: RCSB PDB 5EX5 · PDBe 5EX5 · UniProt P11021
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