SMTL ID : 6zmd.1

Crystal structure of HYPE covalently tethered to BiP bound to AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: G.14, T.15, T.16, Y.17, K.74, E.179, G.204, G.205, G.206, A.207, G.233, E.271, K.274, R.275, S.278, G.341, G.342, S.343, R.345, I.346 Ligands: MG.3, MG.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.15, A:T.15, A:T.16, A:Y.17, A:Y.17, A:K.74, A:E.179, A:G.205, A:G.206, A:A.207, A:G.233, A:E.271, A:E.271, A:K.274, A:S.278, A:S.278, A:G.342 Water bridges: A:E.179, A:D.202, A:G.204

1 x 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(Covalent)

QMK.2: 12 residues within 4Å: Chain A: T.496, G.497 Chain B: L.214, V.215, V.259, H.262, G.269, Y.299, L.302, C.303, N.306 Ligands: PO4.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.299 Hydrogen bonds: B:G.269, B:Y.299, B:N.306 Salt bridges: B:H.262

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.12, G.14, Y.17 Ligands: ANP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:Y.17, H2O.1, H2O.2 MG.4: 3 residues within 4Å: Chain A: E.179, D.202 Ligands: ANP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.179, A:D.202, A:D.202, H2O.1, H2O.1

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: R.79, T.80, D.83, H.455 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.80, A:T.80, A:T.80, A:D.83 Salt bridges: A:H.455 PO4.6: 6 residues within 4Å: Chain B: D.266, G.267, N.268, G.269, R.270 Ligands: QMK.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.267, B:N.268, B:G.269, B:R.270 Salt bridges: B:R.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fauser, J. et al., Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD. Nat Commun (2021)

Release Date

2021-04-14

Peptides

Endoplasmic reticulum chaperone BiP: A
Protein adenylyltransferase FICD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endoplasmic reticulum chaperone BiP

Protein adenylyltransferase FICD