MolNFT v1 · #118235 · protein
Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ADP and inorganic phosphate
5EVZ · 78 kda glucose-regulated protein: “Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ADP and…”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 8 pockets (best druggability 0.77). MolNFT…
- PDB
- 5EVZ
- Type
- protein
- Length
- 763 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein
- UniProt
- P11021
- Ligands
- ADP, MG, PO4
- Pockets
- 8 · best druggability 0.77
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 | 381 | 40% helix, 28% strand | P11021 |
Ligands and binding sites
- ADP · Adenosine-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
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 | 790 | 0.77 | 0.81 | 68 | PO4, MG, ADP |
| 2 | 757 | 0.77 | 0.82 | 72 | MG, PO4, ADP |
| 3 | 968 | 0.73 | 0.76 | 76 | empty |
| 4 | 86 | 0.55 | 0.85 | 29 | empty |
| 5 | 80 | 0.52 | 0.85 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 343 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EVZ · 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 B 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 5EVZ · PDBe 5EVZ · UniProt P11021
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