SMTL ID : 6yx5.1

Structure of DrrA from Legionella pneumophilia in complex with human Rab8a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.20, T.38, D.61 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.20, A:T.38, H2O.1, H2O.1

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 25 residues within 4Å: Chain A: D.14, S.15, G.16, V.17, G.18, K.19, T.20, C.21, F.31, N.32, S.33, T.34, F.35, S.37, T.38, A.63, G.64, N.119, K.120, D.122, V.123, S.149, A.150, K.151 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.16, A:V.17, A:G.18, A:K.19, A:K.19, A:T.20, A:C.21, A:T.34, A:T.38, A:G.64, A:N.119, A:K.120, A:A.150, A:K.151 Water bridges: A:T.20, A:T.20, A:I.36, A:S.37, A:D.61, A:Q.65 Salt bridges: A:D.122 pi-Stacking: A:F.31, A:F.31

3 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.3: 7 residues within 4Å: Chain A: C.121, N.124, R.127, K.131, E.147, I.154, N.155 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.121, A:N.124, A:R.127, A:E.147, A:E.147, A:N.155 Salt bridges: A:K.131 GLC.7: 10 residues within 4Å: Chain B: G.86, S.87, K.90, Q.92, M.171, R.234, D.237, F.238, M.241 Ligands: SO4.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.87, B:Q.92, B:R.234, B:R.234, B:D.237 Salt bridges: B:K.90 GLC.8: 9 residues within 4Å: Chain B: L.174, R.190, K.194, R.244, E.245, N.248, L.249, H.256, L.257 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.174, B:K.194, B:R.244 Water bridges: B:E.245 Salt bridges: B:K.194

1 x LJN: [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Covalent)

LJN.4: 10 residues within 4Å: Chain A: Y.75 Chain B: K.78, D.79, E.81, K.106, P.181, R.182, Y.183, E.184, C.185 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.81 Hydrogen bonds: B:E.81, B:P.181, B:Y.183, B:C.185, A:Y.75 Salt bridges: B:K.78, B:R.182

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

SO4.5: 4 residues within 4Å: Chain A: N.155, V.156, E.157, N.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.155, A:E.157, A:N.158 SO4.6: 3 residues within 4Å: Chain A: Q.65, E.66, R.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66, A:R.67 SO4.9: 4 residues within 4Å: Chain B: G.5, S.6, S.9, K.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.6, B:S.6 Salt bridges: B:K.14 SO4.10: 5 residues within 4Å: Chain B: S.6, L.7, S.18, T.20, A.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.7, B:S.18 SO4.11: 7 residues within 4Å: Chain B: S.87, S.97, K.229, R.234, R.291, E.301 Ligands: GLC.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.87, B:S.87, B:E.301 Water bridges: B:R.291 Salt bridges: B:R.234, B:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, J. et al., Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Ras-related protein Rab-8A: A
Multifunctional virulence effector protein DrrA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ras-related protein Rab-8A

Multifunctional virulence effector protein DrrA