SMTL ID : 1tu3.3 (2 other biounits)

Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.21, T.39, D.62 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.21, A:T.39, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain C: S.21, T.39, D.62 Ligands: GNP.4 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.21, C:T.39, H2O.4, H2O.4

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

GNP.2: 25 residues within 4Å: Chain A: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, F.32, H.33, E.34, Q.36, S.38, T.39, T.63, A.64, G.65, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.17, A:V.18, A:G.19, A:K.20, A:K.20, A:S.21, A:S.22, A:S.22, A:H.33, A:T.39, A:T.39, A:T.63, A:G.65, A:N.120, A:K.121, A:K.121, A:A.151, A:K.152 Water bridges: A:S.21, A:E.37 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32 GNP.4: 25 residues within 4Å: Chain C: E.15, S.16, A.17, V.18, G.19, K.20, S.21, S.22, F.32, H.33, E.34, Q.36, S.38, T.39, T.63, A.64, G.65, N.120, K.121, D.123, L.124, S.150, A.151, K.152 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:A.17, C:V.18, C:G.19, C:K.20, C:K.20, C:S.21, C:S.22, C:S.22, C:H.33, C:T.39, C:T.63, C:G.65, C:N.120, C:K.121, C:K.121, C:A.151, C:K.152 Water bridges: C:S.21, C:E.37, C:T.39, C:T.39 Salt bridges: C:D.123 pi-Stacking: C:F.32, C:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G. et al., Structural basis of Rab5-Rabaptin5 interaction in endocytosis. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-10-05

Peptides

Ras-related protein Rab-5A: AC
Rab GTPase binding effector protein 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
E

B
J

D
J

Ras-related protein Rab-5A

Rab GTPase binding effector protein 1

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