SMTL ID : 1yu9.2 (1 other biounit)

GppNHp-Bound Rab4A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.25, T.43 Ligands: GNP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.25, A:T.43, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: S.25, T.43 Ligands: GNP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.25, B:T.43, H2O.10, H2O.10

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Q.70, E.71, R.72 Chain B: P.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.71, A:R.72 Water bridges: A:Q.70, A:Q.70 Salt bridges: A:R.72 SO4.3: 3 residues within 4Å: Chain A: R.72 Chain B: G.1, P.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.1 Water bridges: A:Q.70, A:R.72, A:R.72 Salt bridges: A:R.72 SO4.6: 4 residues within 4Å: Chain A: P.2 Chain B: Q.70, E.71, R.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.71, B:R.72 Water bridges: B:Q.70, B:Q.70 Salt bridges: B:R.72 SO4.7: 3 residues within 4Å: Chain A: G.1, P.2 Chain B: R.72 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.70, B:R.72, B:R.72 Salt bridges: B:R.72 Hydrogen bonds: A:G.1

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

GNP.4: 23 residues within 4Å: Chain A: N.19, A.20, G.21, T.22, G.23, K.24, S.25, C.26, F.36, S.40, N.41, H.42, T.43, A.68, G.69, N.124, K.125, D.127, L.128, S.154, A.155, L.156 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:G.21, A:T.22, A:T.22, A:G.23, A:K.24, A:K.24, A:S.25, A:S.25, A:C.26, A:S.40, A:N.41, A:H.42, A:T.43, A:G.69, A:N.124, A:K.125, A:A.155, A:L.156 Water bridges: A:S.40, A:S.40, A:T.43, A:D.66, A:Q.70, A:Q.70, A:K.125, A:K.125, A:K.125 Salt bridges: A:D.127 pi-Stacking: A:F.36, A:F.36 GNP.8: 23 residues within 4Å: Chain B: N.19, A.20, G.21, T.22, G.23, K.24, S.25, C.26, F.36, S.40, N.41, H.42, T.43, A.68, G.69, N.124, K.125, D.127, L.128, S.154, A.155, L.156 Ligands: MG.5 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:G.21, B:T.22, B:G.23, B:K.24, B:K.24, B:S.25, B:S.25, B:C.26, B:S.40, B:N.41, B:T.43, B:T.43, B:G.69, B:N.124, B:K.125, B:A.155, B:L.156 Water bridges: B:S.25, B:S.40, B:S.40, B:D.66, B:Q.70, B:Q.70, B:K.125, B:K.125, B:K.125 Salt bridges: B:D.127 pi-Stacking: B:F.36, B:F.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eathiraj, S. et al., Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Nature (2005)

Release Date

2005-07-26

Peptides

GTP-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GTP-binding protein

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