SMTL ID : 7b80.1

DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 17 residues within 4Å: Chain A: T.492 Chain B: E.132, V.214, H.217, H.254, V.258, D.265, G.266, N.267, G.268, R.272, Y.297, Y.298, L.301, E.302, N.305 Ligands: MG.11 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.132, B:H.217, B:D.265, B:G.266, B:N.267, B:N.267, B:G.268, B:R.272, B:Y.297, B:Y.297, B:N.305, B:N.305, A:T.492 Water bridges: B:H.216, B:D.265, B:R.269, A:K.490

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.175, D.198 Ligands: PO4.3, K.4 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: D.265 Ligands: AMP.1 6 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: B:D.265, AMP.1, H2O.5, H2O.7, H2O.15, H2O.16

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

PO4.3: 11 residues within 4Å: Chain A: G.10, T.11, K.70, P.147, E.175, G.200, G.201, G.202, A.203 Ligands: MG.2, K.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.11, A:T.11, A:G.202, A:A.203, A:A.203 Water bridges: A:T.12, A:K.70 Salt bridges: A:K.70

3 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: E.175, D.198, G.200, A.203 Ligands: MG.2, PO4.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.198, A:A.203, H2O.1, H2O.3 K.5: 4 residues within 4Å: Chain A: Q.84, H.226, D.231 Ligands: K.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.226, A:H.226, A:D.231, H2O.11, H2O.11 K.6: 3 residues within 4Å: Chain A: D.224, H.226 Ligands: K.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.226, H2O.4, H2O.11, H2O.12, H2O.13

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.7: 7 residues within 4Å: Chain B: F.232, W.235, L.252, Y.255, K.256, Y.259, I.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.256, B:K.256 P33.8: 5 residues within 4Å: Chain B: R.20, E.49, E.50, D.51, R.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.51

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 4 residues within 4Å: Chain B: R.193, R.194, G.197, Y.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.193, B:R.193 PEG.10: 5 residues within 4Å: Chain B: D.97, V.100, K.101, A.282, Y.284 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perera, L.A. et al., Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD. Nat Commun (2021)

Release Date

2021-07-07

Peptides

Endoplasmic reticulum chaperone BiP: A
Protein adenylyltransferase FICD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Endoplasmic reticulum chaperone BiP

Protein adenylyltransferase FICD

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