SMTL ID : 3e5h.1 (1 other biounit)

Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.20, T.38 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.20, A:T.38, H2O.5, H2O.7 MG.5: 3 residues within 4Å: Chain B: T.20, T.38 Ligands: GNP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.20, B:T.38, H2O.13, H2O.15

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 23 residues within 4Å: Chain A: D.14, G.15, S.17, G.18, K.19, T.20, S.21, F.31, G.32, K.33, Y.35, Q.37, T.38, G.64, G.65, N.123, K.124, D.126, L.127, S.153, A.154, K.155 Ligands: MG.1 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.15, A:S.17, A:G.18, A:K.19, A:K.19, A:T.20, A:S.21, A:S.21, A:G.32, A:T.38, A:T.38, A:G.65, A:N.123, A:K.124, A:K.124, A:A.154, A:K.155 Water bridges: A:T.20, A:T.20, A:K.36, A:K.36, A:Q.37, A:T.38, A:Q.66, A:K.155 Salt bridges: A:D.126 pi-Stacking: A:F.31, A:F.31 GNP.6: 23 residues within 4Å: Chain B: D.14, G.15, S.17, G.18, K.19, T.20, S.21, F.31, G.32, K.33, Y.35, Q.37, T.38, G.64, G.65, N.123, K.124, D.126, L.127, S.153, A.154, K.155 Ligands: MG.5 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:G.15, B:S.17, B:G.18, B:K.19, B:K.19, B:T.20, B:S.21, B:S.21, B:G.32, B:Y.35, B:T.38, B:G.65, B:N.123, B:K.124, B:K.124, B:A.154, B:K.155 Water bridges: B:T.20, B:K.36, B:K.36, B:Q.37, B:T.38, B:T.38, B:Q.66, B:K.155 Salt bridges: B:D.126 pi-Stacking: B:F.31, B:F.31

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.49, L.50, P.51, G.52, N.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.50, A:G.52, A:N.53 Water bridges: A:N.53 GOL.4: 5 residues within 4Å: Chain A: D.126, L.127, E.128, H.129, M.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.126, A:H.129 GOL.7: 5 residues within 4Å: Chain B: T.49, L.50, P.51, G.52, N.53 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.50, B:G.52, B:N.53 Water bridges: B:N.53 GOL.8: 5 residues within 4Å: Chain B: D.126, L.127, E.128, H.129, M.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.126, B:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.H. et al., Large nucleotide-dependent conformational change in Rab28. Febs Lett. (2008)

Release Date

2008-08-26

Peptides

Ras-related protein Rab-28: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ras-related protein Rab-28

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