SMTL ID : 2bcg.1

Structure of doubly prenylated Ypt1:GDI complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GER: GERAN-8-YL GERAN(Non-covalent)

GER.1: 10 residues within 4Å: Chain A: P.130, A.136, K.147, L.154, F.194, M.199, C.223, V.226, A.227 Ligands: GER.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.130, A:L.154, A:F.194, A:F.194, A:V.226, A:A.227 GER.2: 11 residues within 4Å: Chain A: A.136, K.147, R.148, M.150, K.151, L.154, E.155, I.157, S.158, C.223 Ligands: GER.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.136, A:K.147, A:K.147, A:R.148, A:L.154, A:L.154, A:E.155, A:I.157

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: S.22, D.63 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.22, H2O.33, H2O.33, H2O.33, H2O.33

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

GDP.4: 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.3 24 PLIP interactions: 24 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:Y.37, B:T.64 Salt bridges: B:K.21, B:D.124 pi-Stacking: B:Y.33, B:Y.33

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 1 residues within 4Å: Chain B: D.141 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.141 Water bridges: B:K.137, B:K.137, B:K.137, B:D.141, B:D.141, B:D.141, B:M.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pylypenko, O. et al., Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling. Embo J. (2006)

Release Date

2006-01-17

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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