SMTL ID : 5lo8.1 (1 other biounit)

The C2B domain of Rabphilin 3A in complex with PI(4,5)P2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: M.52, D.53, D.113, D.115, D.121 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.52, A:D.53, A:D.113, A:D.115, A:D.121 CA.2: 7 residues within 4Å: Chain A: D.53, D.59, D.113, Y.114, D.115 Ligands: CA.1, SO4.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.53, A:D.59, A:D.113, A:Y.114, A:D.115

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: I.44, N.90, E.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.92, A:E.92 GOL.4: 5 residues within 4Å: Chain A: K.81, T.84, N.86, P.87, E.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.88, A:E.88 GOL.5: 2 residues within 4Å: Chain A: N.159, N.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.159, A:N.161 GOL.6: 2 residues within 4Å: Chain A: E.91, E.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.91

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

SO4.7: 5 residues within 4Å: Chain A: D.53, D.115, I.116, G.117 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.116, A:G.117

1 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.8: 4 residues within 4Å: Chain A: K.63, K.72, K.75, K.77 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.72, A:K.75, A:K.75 Water bridges: A:N.120 Salt bridges: A:K.63, A:K.63, A:K.72, A:K.75, A:K.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrer-Orta, C. et al., Structural characterization of the Rabphilin-3A-SNAP25 interaction. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-06-21

Peptides

Rabphilin-3A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Rabphilin-3A

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