SMTL ID : 6i7j.1

Crystal structure of monomeric FICD mutant L258D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: H.261, I.264, D.265, G.266, N.267, G.268 Ligands: SO4.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.266, A:N.267, A:N.267, A:G.268 Salt bridges: A:H.261 SO4.2: 3 residues within 4Å: Chain A: T.137, L.138, S.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.139, A:S.139, A:S.139 Water bridges: A:L.138, A:L.138 SO4.3: 4 residues within 4Å: Chain A: R.193, R.194, G.197, Y.198 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.193, A:G.197 Salt bridges: A:R.193 SO4.4: 3 residues within 4Å: Chain A: D.97, K.101, Y.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.97, A:Y.284 Salt bridges: A:K.101 SO4.5: 3 residues within 4Å: Chain A: S.139, E.140, H.143 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.143 SO4.6: 5 residues within 4Å: Chain A: V.258, G.268, Y.297 Ligands: SO4.1, PG4.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.132, A:R.272 SO4.7: 4 residues within 4Å: Chain A: R.294, Y.297, Y.298 Ligands: PG4.13 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.294

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 10 residues within 4Å: Chain A: Q.228, E.231, F.232, W.235, L.252, Y.255, K.256, Y.259, I.260 Ligands: PG4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.256 1PE.9: 7 residues within 4Å: Chain A: R.114, M.117, E.118, Y.121, Y.122, L.145, H.166 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.166 1PE.10: 6 residues within 4Å: Chain A: R.290, T.322, D.325, T.326, F.329 Ligands: PEG.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.322, A:D.325

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 6 residues within 4Å: Chain A: Y.59, R.63, D.296, H.299, V.300, A.303 No protein-ligand interaction detected (PLIP) PG4.12: 7 residues within 4Å: Chain A: Y.255, K.256, Y.259, A.304, G.307, V.309 Ligands: 1PE.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.255, A:K.256, A:K.256 PG4.13: 9 residues within 4Å: Chain A: V.214, H.217, V.258, Y.259, Y.298, E.302, N.305 Ligands: SO4.6, SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305 PG4.16: 9 residues within 4Å: Chain A: V.103, M.104, I.106, K.108, L.113, M.117, M.280, Y.284, P.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.280 PG4.17: 5 residues within 4Å: Chain A: G.18, K.19, R.20, E.21, K.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.20, A:E.21

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

PEG.14: 5 residues within 4Å: Chain A: E.3, A.7, Q.10, L.26, M.33 No protein-ligand interaction detected (PLIP) PEG.15: 1 residues within 4Å: Ligands: 1PE.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perera, L.A. et al., An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP. Embo J. (2019)

Release Date

2019-09-25

Peptides

Adenosine monophosphate-protein transferase FICD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenosine monophosphate-protein transferase FICD

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