SMTL ID : 4z8y.2 (1 other biounit)

Crystal structure of Rab GTPase Sec4p mutant - S29V

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: D.11, V.12, G.13, V.14, G.15, K.16, S.17, C.18, F.28, P.30, N.116, K.117, D.119, M.120, S.145, A.146, K.147 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:C.18, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147, A:K.147 Water bridges: A:K.16, A:K.16, A:K.16, A:S.17, A:S.17, A:S.17, A:S.17, A:S.17, A:S.17, A:P.30, A:K.147 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.17, D.58 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.3, H2O.4, H2O.4

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: D.26, D.149 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.26, A:D.26, A:D.149, H2O.3 ZN.4: 1 residues within 4Å: Chain A: E.165 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.165, H2O.2, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldi, F.C. et al., New insights into the molecular mechanism of the Rab GTPase Sec4p activation. Bmc Struct.Biol. (2015)

Release Date

2015-10-14

Peptides

Ras-related protein SEC4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ras-related protein SEC4

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