Research workbench
Crystal structure of ATPase domain of human GRP78 bound to VER155008
Analyse Crystal structure of ATPase domain of human GRP78 bound to VER155008 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CZ1
- Type
- protein
- Length
- 762 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
- 3FD, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 27% 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 | 380 | 40% helix, 26% strand | P11021 |
Ligands and binding sites
- 3FD · 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl) methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile · 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.75 | 0.80 | 74 | 3FD, MG |
| 2 | 158 | 0.75 | 0.92 | 30 | empty |
| 3 | 667 | 0.73 | 0.80 | 66 | 3FD, MG |
| 4 | 435 | 0.70 | 0.81 | 44 | empty |
| 5 | 111 | 0.49 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6CZ1 · Crystal structure of ATPase domain of Human GRP78 bound to Ver155008 · 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 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 P11021
- Elsewhere: RCSB PDB 6CZ1 · PDBe 6CZ1 · UniProt P11021
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