SMTL ID : 1s8f.3 (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-tetramer

Ligands

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

SR.1: 3 residues within 4Å: Chain A: S.23 Ligands: GDP.2, BEZ.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1 SR.7: 7 residues within 4Å: Chain B: F.71, R.72, S.73 Chain D: F.71, R.72, S.73 Ligands: SR.17 No protein-ligand interaction detected (PLIP) SR.11: 3 residues within 4Å: Chain C: S.23 Ligands: GDP.12, BEZ.15 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.23, H2O.10, H2O.10, H2O.10 SR.17: 7 residues within 4Å: Chain B: F.71, R.72, S.73 Chain D: F.71, R.72, S.73 Ligands: SR.7 No protein-ligand interaction detected (PLIP)

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

GDP.2: 19 residues within 4Å: Chain A: D.17, G.18, G.19, V.20, G.21, K.22, S.23, S.24, F.34, D.64, N.126, K.127, D.129, I.130, S.156, A.157, K.158 Ligands: SR.1, BEZ.5 25 PLIP interactions: 25 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:S.156, A:A.157, A:K.158 Water bridges: A:K.22, A:K.22, A:S.23, A:S.23, A:T.36, A:T.36, A:T.36, A:T.65 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 GDP.12: 19 residues within 4Å: Chain C: D.17, G.18, G.19, V.20, G.21, K.22, S.23, S.24, F.34, D.64, N.126, K.127, D.129, I.130, S.156, A.157, K.158 Ligands: SR.11, BEZ.15 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.19, C:V.20, C:G.21, C:K.22, C:S.23, C:S.24, C:S.24, C:N.126, C:K.127, C:K.127, C:S.156, C:A.157, C:K.158 Water bridges: C:K.22, C:K.22, C:S.23, C:S.23, C:T.36, C:T.36, C:T.36, C:T.65 Salt bridges: C:K.22, C:D.129 pi-Stacking: C:F.34, C:F.34 GDP.19: 17 residues within 4Å: Chain D: 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.16 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:G.19, D:V.20, D:G.21, D:K.22, D:S.23, D:S.24, D:S.24, D:N.126, D:K.127, D:K.127, D:A.157, D:K.158 Water bridges: D:K.22, D:K.22, D:K.22, D:K.22, D:S.23, D:S.23, D:S.23, D:S.24 Salt bridges: D:K.22, D:D.129 pi-Stacking: D:F.34, D:F.34

8 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.3: 9 residues within 4Å: Chain A: R.72, S.73 Chain C: R.70, F.71, S.73, L.74 Chain D: S.73, L.74 Ligands: BEZ.14 9 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 1 interactions with chain D Water bridges: A:R.72, A:R.72, C:R.70 Salt bridges: A:R.72, C:R.70 Hydrophobic interactions: C:F.71, C:F.71, C:L.74, D:L.74 BEZ.4: 7 residues within 4Å: Chain A: I.42, R.70 Chain B: W.63, L.74, P.77, F.78 Ligands: BEZ.13 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.42, B:W.63, B:L.74, B:P.77, B:P.77 Water bridges: A:R.70 Salt bridges: A:R.70 BEZ.5: 7 residues within 4Å: Chain A: H.40, T.41, I.42, Q.68 Chain B: F.46 Ligands: SR.1, GDP.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.40, A:I.42, B:F.46, B:F.46 Water bridges: A:G.19, A:S.23, A:S.23, A:S.23, A:T.41, A:T.41, A:T.65, A:G.67 Salt bridges: A:H.40 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 BEZ.13: 9 residues within 4Å: Chain A: R.70, F.71, S.73, L.74 Chain B: S.73, L.74 Chain C: R.72, S.73 Ligands: BEZ.4 9 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.71, A:F.71, A:L.74, B:L.74 Water bridges: A:R.70, C:R.72, C:R.72 Salt bridges: A:R.70, C:R.72 BEZ.14: 7 residues within 4Å: Chain C: I.42, R.70 Chain D: W.63, L.74, P.77, F.78 Ligands: BEZ.3 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.63, D:L.74, D:P.77, D:P.77, C:I.42 Water bridges: C:R.70 Salt bridges: C:R.70 BEZ.15: 7 residues within 4Å: Chain C: H.40, T.41, I.42, Q.68 Chain D: F.46 Ligands: SR.11, GDP.12 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.40, C:I.42, D:F.46, D:F.46 Water bridges: C:G.19, C:S.23, C:S.23, C:S.23, C:T.41, C:T.41, C:T.65, C:G.67 Salt bridges: C:H.40 BEZ.20: 9 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:V.44, D:T.65, D:E.69, D:L.74, D:R.75, D:F.78 Water bridges: D:R.75, D:R.75 Salt bridges: D:R.75

2 x MG: MAGNESIUM ION(Non-covalent)

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.6, H2O.6, H2O.6, H2O.6 MG.16: 3 residues within 4Å: Chain D: S.23, E.45 Ligands: GDP.19 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.23, H2O.15, H2O.15, H2O.15, H2O.15

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

CL.8: 4 residues within 4Å: Chain B: R.72, R.75, T.76, Y.110 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: R.72, R.75, T.76, Y.110 Ligand excluded by PLIP

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Ras-related protein Rab-9A

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