SMTL ID : 7bwt.1

SopD-Rab8 complex structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 9 residues within 4Å: Chain A: S.159, E.162, S.263, M.264, Y.297, Y.300, H.301 Chain B: A.75, R.78 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.159, A:E.162, A:M.264, A:M.264, A:Y.297, B:R.78 PEG.2: 3 residues within 4Å: Chain A: S.287, G.288, K.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.291 Water bridges: A:S.150

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.231, S.232, G.240, N.241, F.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.232, A:N.241, A:F.242 GOL.4: 5 residues within 4Å: Chain A: K.104, I.120, Q.164, L.167, E.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.104 Water bridges: A:E.171, A:E.171 GOL.5: 7 residues within 4Å: Chain A: S.159, E.161, E.162, M.208, M.209, S.263 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.159, A:S.159, A:E.161, A:S.263, A:S.263 Water bridges: A:E.162, A:Q.254 GOL.6: 6 residues within 4Å: Chain A: E.161, E.207, M.208, P.211, Q.254 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.208 Water bridges: A:M.208, A:Q.254, A:Q.254 GOL.7: 2 residues within 4Å: Chain A: I.79, E.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.79, A:E.86 Water bridges: A:V.92 GOL.10: 8 residues within 4Å: Chain B: R.26, F.27, D.30, R.47, N.154, V.157, E.158 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.27, B:D.30, B:N.154, B:E.158 GOL.11: 4 residues within 4Å: Chain B: K.9, W.61, T.63, Y.76 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.9, B:K.9, B:T.63, B:T.63, B:Y.76, B:Y.76 GOL.12: 5 residues within 4Å: Chain A: E.259 Chain B: S.28, E.29, I.46, R.47 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.259, A:E.259, B:E.29 Water bridges: B:I.46 GOL.13: 5 residues within 4Å: Chain B: F.27, S.28, D.30, R.47 Ligands: GOL.10 No protein-ligand interaction detected (PLIP)

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

GDP.8: 18 residues within 4Å: Chain B: D.15, S.16, G.17, V.18, G.19, K.20, T.21, C.22, F.32, N.33, N.120, K.121, D.123, V.124, S.150, A.151, K.152 Ligands: MG.9 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.17, B:V.18, B:G.19, B:K.20, B:T.21, B:C.22, B:N.33, B:N.120, B:K.121, B:K.121, B:S.150, B:A.151, B:K.152 Water bridges: B:K.20, B:K.20, B:K.20, B:T.21, B:T.21, B:T.21 Salt bridges: B:K.20, B:D.123 pi-Stacking: B:F.32, B:F.32 pi-Cation interactions: B:K.121

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: T.21, D.62 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.21, H2O.4, H2O.4, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lian, H. et al., The Salmonella effector protein SopD targets Rab8 to positively and negatively modulate the inflammatory response. Nat Microbiol (2021)

Release Date

2021-02-24

Peptides

SPI-1 type III secretion system effector SopD: A
Ras-related protein Rab-8A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SPI-1 type III secretion system effector SopD

Ras-related protein Rab-8A