Research workbench
Crystal structure of human GRP78 in complex with 8-aminoadenosine
Analyse Crystal structure of human GRP78 in complex with 8-aminoadenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DFM
- Type
- protein
- Length
- 764 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
- P11021
- Ligands
- 3BH
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 382 | 41% helix, 28% strand | P11021 |
Ligands and binding sites
- 3BH · (2R,3R,4S,5R)-2-(6,8-diaminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.77 | 0.92 | 37 | 3BH |
| 2 | 236 | 0.77 | 0.91 | 37 | 3BH |
| 3 | 381 | 0.65 | 0.79 | 32 | empty |
| 4 | 417 | 0.61 | 0.76 | 39 | empty |
| 5 | 264 | 0.49 | 0.74 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DFM · Crystal structure of human GRP78 in complex with 8-aminoadenosine · 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 0.89
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 6DFM · PDBe 6DFM · UniProt P11021
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