Research workbench
Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6- amino-8-((2-CHLOROBENZYL)AMINO)-9H-purin-9-yl)-5-(hydroxymethyl) tetrahydrofuran-3,4-diol
Analyse Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWS
- Type
- protein
- Length
- 763 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
- HFY, MG
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 382 | 40% helix, 29% strand | P11021 |
| B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 381 | 40% helix, 27% strand | P11021 |
Ligands and binding sites
- HFY · 8-{[(2-chlorophenyl)methyl]amino}adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.78 | 0.93 | 26 | empty |
| 2 | 717 | 0.76 | 0.81 | 66 | HFY, MG |
| 3 | 716 | 0.76 | 0.81 | 69 | HFY, MG |
| 4 | 386 | 0.70 | 0.82 | 37 | empty |
| 5 | 88 | 0.46 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 7 hydrogen bonds · protein-protein
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 P11021
- Elsewhere: RCSB PDB 6DWS · PDBe 6DWS · UniProt P11021
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