SMTL ID : 8alk.1

Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.88, D.237, D.377 Ligands: CA.2, OJU.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.88, A:D.237, A:D.377, H2O.1, H2O.3 CA.2: 4 residues within 4Å: Chain A: D.88, G.89 Ligands: CA.1, OJU.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.88, A:G.89, H2O.1, H2O.1, H2O.1 CA.3: 3 residues within 4Å: Chain A: D.173, D.237 Ligands: OJU.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.173, A:D.237, H2O.1, H2O.1, H2O.3 CA.5: 4 residues within 4Å: Chain B: S.23, D.45, D.64 Ligands: GDP.4 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, B:D.64, H2O.3, H2O.3, H2O.3

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 18 residues within 4Å: Chain B: D.17, S.18, G.19, V.20, G.21, K.22, S.23, C.24, Y.34, D.64, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: CA.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:S.23, B:C.24, B:N.122, B:K.123, B:K.123, B:A.153, B:K.154 Water bridges: B:K.22, B:K.22, B:S.23, B:Y.34, B:Y.34 Salt bridges: B:K.22, B:D.125 pi-Stacking: B:Y.34, B:Y.34

1 x OJU: 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium(Covalent)

OJU.6: 14 residues within 4Å: Chain A: L.51, D.88, G.89, L.90, G.91, G.92, G.93, S.372, C.374, D.377 Chain B: T.77 Ligands: CA.1, CA.2, CA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.91 Salt bridges: A:D.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaspers, M.S. et al., Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b. Nat Commun (2023)

Release Date

2023-04-12

Peptides

Phosphocholine hydrolase Lem3: A
Ras-related protein Rab-1B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphocholine hydrolase Lem3

Ras-related protein Rab-1B