SMTL ID : 9mf1.1

Crystal structure of RIT1 in the GDP state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

GDP.1: 16 residues within 4Å: Chain A: A.29, G.31, V.32, G.33, K.34, S.35, A.36, F.46, N.134, K.135, D.137, L.138, S.164, A.165, A.166 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.31, A:V.32, A:G.33, A:K.34, A:S.35, A:A.36, A:N.134, A:K.135, A:K.135, A:A.165, A:A.166 Water bridges: A:K.34, A:S.35, A:P.47, A:P.47, A:D.49, A:T.76 Salt bridges: A:K.34, A:D.137 pi-Stacking: A:F.46, A:F.46

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.35 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.35, H2O.2, H2O.2, H2O.2, H2O.3

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.41, H.44, I.60, I.62, R.168, D.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.168, A:D.172 Water bridges: A:R.168, A:R.168 GOL.4: 4 residues within 4Å: Chain A: R.168, Y.169, Y.170, D.173 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.168, A:Y.170, A:Y.170, A:I.171 Water bridges: A:D.172, A:D.172 GOL.5: 4 residues within 4Å: Chain A: K.146, F.161, E.162, Y.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.146, A:E.162 GOL.6: 3 residues within 4Å: Chain A: A.80, E.81, F.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.81, A:F.82 Water bridges: A:F.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dharmaiah, S. et al., Structure based mechanism of LZTR1-mediated recognition of RAS GTPases. Science (2025)

Release Date

2025-09-10

Peptides

GTP-binding protein Rit1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTP-binding protein Rit1

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