SMTL ID : 5low.2 (1 other biounit)

Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.53, D.59, D.113, Y.114, D.115 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.53, A:D.59, A:D.113, A:D.115, H2O.1 CA.2: 3 residues within 4Å: Chain A: M.52, D.115, D.121 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.52, A:D.115, A:D.121, H2O.1 CA.3: 6 residues within 4Å: Chain B: D.53, D.59, D.113, Y.114, D.115 Ligands: CA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.59, B:Y.114, B:D.115 CA.4: 6 residues within 4Å: Chain B: M.52, D.53, D.113, D.115, D.121 Ligands: CA.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:M.52, B:D.53, B:D.113, B:D.121 CA.5: 4 residues within 4Å: Chain C: M.52, D.53, D.115, D.121 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.52, C:D.53, C:D.115, C:D.121, H2O.1 CA.6: 5 residues within 4Å: Chain C: D.53, D.59, D.113, Y.114, D.115 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.53, C:D.59, C:Y.114, C:D.115

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: Y.32, K.98, H.99 Chain D: R.72 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.32, A:Y.32, A:H.99, D:R.72 GOL.8: 5 residues within 4Å: Chain F: D.32, A.35, D.36, L.39 Chain G: E.22 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:D.36, G:E.22 GOL.9: 1 residues within 4Å: Chain F: R.30 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.28 GOL.10: 3 residues within 4Å: Chain G: T.69, D.72, Q.76 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.76, G:Q.76

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: ABC
Synaptosomal-associated protein 25: DF
Synaptosomal-associated protein 25: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

F
M

E
L

G
N

Rabphilin-3A

Synaptosomal-associated protein 25

Synaptosomal-associated protein 25

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