SMTL ID : 3pz2.1

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: D.237, C.239, H.289 Ligands: 3PZ.3, GRG.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.237, B:D.237, B:C.239, B:H.289

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain B: H.63, M.65 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.63, B:M.65

1 x 3PZ: (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile(Non-covalent)

3PZ.3: 13 residues within 4Å: Chain A: D.63 Chain B: Y.43, L.44, W.51, D.237, C.239, W.243, D.286, P.287, F.288, H.289 Ligands: ZN.1, GRG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.51, B:W.51, B:W.243, B:F.288 Hydrogen bonds: B:Y.43, B:F.288 pi-Stacking: B:F.288, B:F.288

1 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.4: 23 residues within 4Å: Chain A: K.107, Y.109, F.145 Chain B: Y.50, L.95, Q.102, R.143, F.146, H.189, G.191, Q.192, Y.194, C.195, R.231, K.234, C.239, Y.240, W.242, W.243, F.292, C.313 Ligands: ZN.1, 3PZ.3 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.95, B:R.143, B:F.146, B:Y.194, B:Y.240, B:F.292 Hydrogen bonds: B:R.231 Water bridges: B:G.230, B:K.234, B:L.235, A:K.107, A:K.107, A:K.107 Salt bridges: B:H.189, B:R.231, B:K.234, B:K.234, A:K.107, A:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bon, R.S. et al., Structure-Guided Development of Selective RabGGTase Inhibitors. Angew.Chem.Int.Ed.Engl. (2011)

Release Date

2011-05-11

Peptides

Geranylgeranyl transferase type-2 subunit alpha: A
Geranylgeranyl transferase type-2 subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl transferase type-2 subunit alpha

Geranylgeranyl transferase type-2 subunit beta

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