SMTL ID : 3tso.1

Structure of the cancer associated Rab25 protein in complex with FIP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.24, T.42, D.65 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.3, H2O.3 MG.8: 3 residues within 4Å: Chain B: T.24, T.42 Ligands: GNP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.24, B:T.42, H2O.6, H2O.6

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

GNP.2: 24 residues within 4Å: Chain A: S.19, G.20, V.21, G.22, K.23, T.24, N.25, F.35, S.36, H.37, D.38, S.39, T.41, T.42, A.67, G.68, N.123, K.124, D.126, L.127, S.153, A.154, L.155 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.19, A:G.20, A:V.21, A:G.22, A:K.23, A:K.23, A:T.24, A:T.24, A:N.25, A:S.36, A:T.42, A:T.42, A:G.68, A:N.123, A:K.124, A:K.124, A:S.153, A:A.154, A:L.155 Water bridges: A:T.24, A:R.40 Salt bridges: A:D.126 pi-Stacking: A:F.35, A:F.35 pi-Cation interactions: A:K.124 GNP.9: 24 residues within 4Å: Chain B: E.18, S.19, G.20, V.21, G.22, K.23, T.24, N.25, F.35, S.36, H.37, S.39, T.41, T.42, A.67, G.68, N.123, K.124, D.126, L.127, S.153, A.154, L.155 Ligands: MG.8 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.20, B:V.21, B:G.22, B:K.23, B:K.23, B:T.24, B:N.25, B:S.36, B:S.39, B:R.40, B:T.41, B:T.42, B:T.42, B:G.68, B:N.123, B:K.124, B:K.124, B:A.154, B:L.155 Water bridges: B:T.24, B:T.24 Salt bridges: B:D.126 pi-Stacking: B:F.35, B:F.35

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.29, N.33, E.34, F.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:F.35, A:F.35 GOL.4: 9 residues within 4Å: Chain A: T.42, I.43, G.44, L.69, R.71, R.73 Chain D: E.41, I.44, D.45 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.42, A:G.44, A:R.71, A:R.73, A:R.73 GOL.5: 10 residues within 4Å: Chain A: I.16, T.66, A.67, L.69, R.73, T.76, Y.79, Y.80, W.104, E.107 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.69, A:L.69, A:R.73, A:T.76, A:Y.80, A:Y.80 Water bridges: A:Y.79 GOL.10: 9 residues within 4Å: Chain B: T.42, I.43, G.44, L.69, R.71, R.73 Chain C: E.41, I.44, D.45 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.42, B:G.44, B:R.71, B:R.73 Water bridges: B:T.66, B:R.71 GOL.11: 9 residues within 4Å: Chain B: I.16, T.66, A.67, L.69, R.73, T.76, Y.80, W.104, E.107 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.67, B:L.69, B:R.73, B:T.76, B:Y.80, B:Y.80 Water bridges: B:Y.79

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 3 residues within 4Å: Chain A: E.161, L.162, E.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.162 Water bridges: A:N.159 PO4.7: 5 residues within 4Å: Chain A: Y.98, A.99, V.101, E.102, F.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.98, A:A.99, A:V.101, A:E.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oda, S. et al., Structure of the cancer associated Rab25 protein in complex with FIP2. TO BE PUBLISHED

Release Date

2012-09-19

Peptides

Ras-related protein Rab-25: AB
Rab11 family-interacting protein 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ras-related protein Rab-25

Rab11 family-interacting protein 2