MolNFT v1 · #146379 · protein
Crystal structure of human GRP78 in complex with 8-bromoadenosine
6DFO · Endoplasmic reticulum chaperone bip: “Crystal structure of human GRP78 in complex with 8-bromoadenosine”. X-ray diffraction, 1 ligand (GBA), 9 pockets (best druggability 0.77). MolNFT v1 #146379 on GenesisL1: 3D structure, binding…
- PDB
- 6DFO
- 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
- GBA
- Pockets
- 9 · best druggability 0.77
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 | 380 | 40% helix, 28% strand | P11021 |
| B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 382 | 40% helix, 28% strand | P11021 |
Ligands and binding sites
- GBA · 8-bromoadenosine · ligand · 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 | 216 | 0.77 | 0.92 | 37 | GBA |
| 2 | 223 | 0.76 | 0.91 | 38 | GBA |
| 3 | 410 | 0.65 | 0.79 | 35 | empty |
| 4 | 422 | 0.64 | 0.78 | 35 | empty |
| 5 | 220 | 0.47 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 108 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DFO · Crystal structure of human GRP78 in complex with 8-bromoadenosine · 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 0.88
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 6DFO · PDBe 6DFO · UniProt P11021
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