SMTL ID : 1s8f.5 (4 other biounits)

Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.23, E.45 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: S.23, E.45 Ligands: GDP.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.4, H2O.4, H2O.4, H2O.5

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.2: 7 residues within 4Å: Chain A: F.71, R.72, S.73 Chain B: F.71, R.72, S.73 Ligands: SR.7 No protein-ligand interaction detected (PLIP) SR.7: 7 residues within 4Å: Chain A: F.71, R.72, S.73 Chain B: F.71, R.72, S.73 Ligands: SR.2 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: R.72, R.75, T.76, Y.110 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.72, R.75, T.76, Y.110 Ligand excluded by PLIP

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

GDP.4: 17 residues within 4Å: Chain A: D.17, G.18, G.19, V.20, G.21, K.22, S.23, S.24, F.34, N.126, K.127, D.129, I.130, S.156, A.157, K.158 Ligands: MG.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.19, A:V.20, A:G.21, A:K.22, A:S.23, A:S.24, A:S.24, A:N.126, A:K.127, A:K.127, A:A.157, A:K.158 Water bridges: A:K.22, A:K.22, A:K.22, A:K.22, A:S.23, A:S.23, A:S.23, A:S.24 Salt bridges: A:K.22, A:D.129 pi-Stacking: A:F.34, A:F.34 GDP.9: 17 residues within 4Å: Chain B: D.17, G.18, G.19, V.20, G.21, K.22, S.23, S.24, F.34, N.126, K.127, D.129, I.130, S.156, A.157, K.158 Ligands: MG.6 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:S.23, B:S.24, B:S.24, B:N.126, B:K.127, B:K.127, B:A.157, B:K.158 Water bridges: B:K.22, B:K.22, B:K.22, B:K.22, B:S.23, B:S.23, B:S.23, B:S.24 Salt bridges: B:K.22, B:D.129 pi-Stacking: B:F.34, B:F.34

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.5: 9 residues within 4Å: Chain A: V.44, T.65, E.69, R.70, F.71, R.72, L.74, R.75, F.78 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.44, A:T.65, A:E.69, A:L.74, A:R.75, A:F.78 Water bridges: A:R.75, A:R.75 Salt bridges: A:R.75 BEZ.10: 9 residues within 4Å: Chain B: V.44, T.65, E.69, R.70, F.71, R.72, L.74, R.75, F.78 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.44, B:T.65, B:E.69, B:L.74, B:R.75, B:F.78 Water bridges: B:R.75, B:R.75 Salt bridges: B:R.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wittmann, J.G. et al., Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II. Febs Lett. (2004)

Release Date

2004-06-11

Peptides

Ras-related protein Rab-9A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Ras-related protein Rab-9A

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