Research workbench
Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with small molecule inhibitor
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
- 3LDP
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein
- UniProt
- P11021
- Ligands
- 3P1
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 78 kda glucose-regulated protein | protein | 381 | 39% helix, 29% strand | P11021 |
Ligands and binding sites
- 3P1 · 8-[(quinolin-2-ylmethyl)amino]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.78 | 0.82 | 76 | 3P1 |
| 2 | 748 | 0.76 | 0.81 | 65 | 3P1 |
| 3 | 972 | 0.75 | 0.78 | 79 | empty |
| 4 | 128 | 0.41 | 0.75 | 21 | empty |
| 5 | 62 | 0.37 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 331 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LDP · 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 0.89
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 3LDP · PDBe 3LDP · UniProt P11021
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