MolNFT v1 · #172310 · protein
Crystal structure of GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ADP and calcium
6ZYH · Endoplasmic reticulum chaperone bip: “Crystal structure of GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ADP and calcium”. X-ray diffraction, 2 ligands (ADP, CA), 5 pockets (best druggability 0.81). MolNFT…
- PDB
- 6ZYH
- Type
- protein
- Length
- 758 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum chaperone bip
- EC
- 3.6.4.10
- UniProt
- G3I8R9
- Ligands
- ADP, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 379 | 40% helix, 29% strand | G3I8R9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.81 | 0.83 | 74 | ADP, CA |
| 2 | 956 | 0.79 | 0.81 | 92 | ADP, CA |
| 3 | 63 | 0.34 | 0.77 | 21 | empty |
| 4 | 66 | 0.34 | 0.77 | 14 | empty |
| 5 | 53 | 0.31 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 673 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ZYH · Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATPase domain in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- G3I8R9 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (G3I8R9) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 6ZYH · PDBe 6ZYH · UniProt G3I8R9
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