SMTL ID : 9jjv.1

Truncated RNF112, transition-like state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: R.49, R.50, G.51, K.52, S.53, F.54, W.86, S.87, P.88, R.186, D.187, H.235, P.236, I.240, T.241, F.255 Ligands: ALF.2, MG.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.49, A:R.50, A:G.51, A:K.52, A:S.53, A:F.54, A:S.87, A:S.87, A:R.186, A:H.235 Water bridges: A:R.49, A:G.89, A:T.94, A:G.122, A:D.187, A:D.187 Salt bridges: A:R.49, A:R.49, A:K.52, A:D.187 pi-Stacking: A:F.54 GDP.5: 18 residues within 4Å: Chain B: R.49, R.50, G.51, K.52, S.53, F.54, W.86, S.87, P.88, R.186, D.187, H.235, P.236, I.240, T.241, F.255 Ligands: ALF.6, MG.8 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:R.49, B:R.50, B:G.51, B:K.52, B:S.53, B:F.54, B:S.87, B:S.87, B:R.186, B:H.235 Water bridges: B:R.49, B:G.89, B:T.94, B:T.94, B:G.122, B:R.186, B:D.187 Salt bridges: B:R.49, B:R.49, B:K.52, B:D.187 pi-Stacking: B:F.54

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 9 residues within 4Å: Chain A: K.48, R.49, K.52, T.92, T.93, T.94, G.122 Ligands: GDP.1, MG.4 No protein-ligand interaction detected (PLIP) ALF.6: 9 residues within 4Å: Chain B: K.48, R.49, K.52, T.92, T.93, T.94, G.122 Ligands: GDP.5, MG.8 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: N.177 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.4, H2O.6, H2O.7, H2O.9, H2O.10 MG.4: 5 residues within 4Å: Chain A: S.53, T.94, D.119 Ligands: GDP.1, ALF.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.53, A:T.94, H2O.4, H2O.5 MG.7: 1 residues within 4Å: Chain B: N.177 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.16, H2O.17, H2O.18, H2O.21, H2O.22 MG.8: 5 residues within 4Å: Chain B: S.53, T.94, D.119 Ligands: GDP.5, ALF.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.53, B:T.94, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, Y.T. et al., Structural and functional characterization of the brain-specific dynamin superfamily member RNF112. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-23

Peptides

LOC432253 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LOC432253 protein

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