MolNFT v1 · #146653 · protein
Crystal structure of human GRP78 in complex with 7-deaza-2'-C- methyladenosine
6DO2 · Endoplasmic reticulum chaperone bip: “Crystal structure of human GRP78 in complex with 7-deaza-2'-C- methyladenosine”. X-ray diffraction, 1 ligand (H5V), 7 pockets (best druggability 0.79). MolNFT v1 #146653 on GenesisL1: 3D…
- PDB
- 6DO2
- 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
- H5V
- Pockets
- 7 · best druggability 0.79
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
- H5V · 7-(2-C-methyl-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine · 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 | 274 | 0.79 | 0.91 | 57 | H5V |
| 2 | 700 | 0.76 | 0.82 | 72 | H5V |
| 3 | 940 | 0.73 | 0.77 | 66 | empty |
| 4 | 464 | 0.68 | 0.80 | 47 | empty |
| 5 | 147 | 0.45 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 384 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6DO2 · Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine · 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 6DO2 · PDBe 6DO2 · UniProt P11021
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.