SMTL ID : 1ukv.1

Structure of RabGDP-dissociation inhibitor in complex with prenylated YPT1 GTPase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain B: S.22, D.63 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.22, H2O.29, H2O.29, H2O.29, H2O.29

1 x GER: GERAN-8-YL GERAN(Covalent)

GER.2: 12 residues within 4Å: Chain A: V.129, P.130, A.136, M.142, K.147, M.150, K.151, L.154, M.199, Y.222, C.223 Chain B: C.206 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.129, A:P.130, A:A.136, A:K.147, A:K.147, A:K.151, A:L.154, A:Y.222

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

GDP.3: 21 residues within 4Å: Chain B: N.16, S.17, G.18, V.19, G.20, K.21, S.22, C.23, Y.33, T.34, D.36, Y.37, E.68, N.121, K.122, D.124, L.125, S.151, A.152, L.153 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:N.16, B:G.18, B:V.19, B:G.20, B:K.21, B:S.22, B:C.23, B:Y.33, B:T.34, B:D.36, B:Y.37, B:N.121, B:K.122, B:K.122, B:A.152, B:L.153 Water bridges: B:S.22, B:S.22, B:S.22, B:Y.37, B:T.64 Salt bridges: B:K.21, B:D.124 pi-Stacking: B:Y.33, B:Y.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rak, A. et al., Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase. Science (2003)

Release Date

2004-09-01

Peptides

Secretory pathway GDP dissociation inhibitor: A
GTP-binding protein YPT1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
Y

Secretory pathway GDP dissociation inhibitor

GTP-binding protein YPT1

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