SMTL ID : 2g77.1

Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: T.43, T.61, D.84 Ligands: GDP.2, AF3.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.43, B:T.61, H2O.11, H2O.16

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

GDP.2: 20 residues within 4Å: Chain A: R.116 Chain B: D.37, S.38, N.39, V.40, G.41, K.42, T.43, C.44, F.54, T.58, N.144, K.145, D.147, L.148, S.174, A.175, K.176 Ligands: MG.1, AF3.3 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.39, B:V.40, B:G.41, B:K.42, B:T.43, B:T.43, B:C.44, B:T.58, B:N.144, B:K.145, B:K.145, B:A.175, B:K.176 Water bridges: B:T.43, B:D.56, B:D.56, B:T.61, B:T.61, B:K.145, B:K.176, B:K.176, B:K.176, A:R.116 Salt bridges: B:K.42, B:D.147, A:R.116, A:R.116 pi-Stacking: B:F.54

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 12 residues within 4Å: Chain A: R.116, Q.151 Chain B: S.38, N.39, K.42, A.60, T.61, T.85, A.86, G.87 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism. Nature (2006)

Release Date

2006-07-25

Peptides

GTPase-activating protein GYP1: A
Ras-related protein Rab-33B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase-activating protein GYP1

Ras-related protein Rab-33B