SMTL ID : 7ezb.1

Thorarchaeota Rab bound to GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: D.14, G.15, A.16, V.17, G.18, K.19, T.20, A.21, F.31, T.33, N.121, K.122, D.124, L.125, S.151, A.152, L.153 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:D.14, A:A.16, A:V.17, A:G.18, A:K.19, A:T.20, A:A.21, A:N.121, A:K.122, A:S.151, A:A.152, A:L.153 Water bridges: A:K.19, A:K.19, A:T.20, A:T.20, A:D.32, A:T.33, A:R.37, A:R.37, A:K.122, A:K.122, A:K.122 Salt bridges: A:K.19, A:D.124 pi-Stacking: A:F.31, A:F.31 GDP.3: 18 residues within 4Å: Chain B: D.14, G.15, A.16, V.17, G.18, K.19, T.20, A.21, F.31, T.33, N.121, K.122, D.124, L.125, S.151, A.152, L.153 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.16, B:V.17, B:G.18, B:K.19, B:T.20, B:T.20, B:A.21, B:N.121, B:K.122, B:K.122, B:S.151, B:A.152, B:L.153 Water bridges: B:K.19, B:T.20, B:T.20, B:D.32, B:G.66, B:Q.67 Salt bridges: B:K.19, B:D.124 pi-Stacking: B:F.31, B:F.31

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.20, R.37, D.63 Ligands: GDP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.20, H2O.1, H2O.2 MG.4: 2 residues within 4Å: Chain B: T.20 Ligands: GDP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.20, H2O.8, H2O.11, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, L.T. et al., The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol (2024)

Release Date

2022-06-08

Peptides

Thorarchaeota Rab: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thorarchaeota Rab

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