Crystal structure of hype covalently tethered to bip bound to AMP-pnp

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).

Ligands and binding sites

• ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
• QMK · ~{N}-[2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,2,3-triazol-4-yl]ethyl]ethanamide · ligand · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A
• PO4 · Phosphate ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1080 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6ZMD · Crystal structure of HYPE covalently tethered to BiP bound to AMP-PNP · 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 0.98
• Q9BVA6 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase ficd (Q9BVA6) · a predicted model of the same protein · chain B against A, TM-score 0.92

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
• Every structure of UniProt Q9BVA6
• Elsewhere: RCSB PDB 6ZMD · PDBe 6ZMD · UniProt P11021 · UniProt Q9BVA6