SMTL ID : 5lob.1

Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-3-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.53, D.59, D.113, Y.114, D.115 Ligands: CA.2, SO4.3 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 CA.2: 7 residues within 4Å: Chain A: M.52, D.53, D.113, D.115, K.118, D.121 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.52, A:D.53, A:D.113, A:D.115, A:D.115 CA.10: 5 residues within 4Å: Chain B: D.53, D.59, D.113, Y.114, D.115 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.53, B:D.59, B:D.113, B:Y.114, B:D.115 CA.11: 6 residues within 4Å: Chain B: M.52, D.53, D.113, D.115, K.118, D.121 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:M.52, B:D.53, B:D.115, B:D.115, B:D.121 CA.15: 7 residues within 4Å: Chain C: D.53, D.59, D.113, Y.114, D.115 Ligands: CA.16, SO4.17 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.53, C:D.53, C:D.113, C:Y.114, C:D.115 CA.16: 6 residues within 4Å: Chain C: M.52, D.53, D.113, D.115, D.121 Ligands: CA.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:M.52, C:D.53, C:D.113, C:D.115, C:D.121

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

SO4.3: 5 residues within 4Å: Chain A: D.53, D.59, D.115, I.116 Ligands: CA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.116 SO4.4: 6 residues within 4Å: Chain A: Q.36, I.40, E.92, F.93, F.94 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:F.93 SO4.5: 3 residues within 4Å: Chain A: H.76, F.94 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.94 Salt bridges: A:H.76 SO4.6: 2 residues within 4Å: Chain A: H.99 Chain D: E.73 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Salt bridges: A:H.99, A:K.147 Hydrogen bonds: D:E.73, D:E.73 SO4.12: 3 residues within 4Å: Chain B: T.84, L.85, N.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.85, B:N.86, B:N.86 SO4.13: 3 residues within 4Å: Chain B: K.118, S.119, N.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.120 SO4.17: 6 residues within 4Å: Chain C: D.53, D.59, Y.114, D.115, I.116 Ligands: CA.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.53, C:I.116 SO4.19: 3 residues within 4Å: Chain E: N.52, H.55, M.56 No protein-ligand interaction detected (PLIP) SO4.20: 6 residues within 4Å: Chain F: D.69, G.72, E.73, D.76 Chain G: E.63 Ligands: SO4.23 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:E.63, F:D.69 SO4.23: 4 residues within 4Å: Chain F: D.76 Chain G: T.66, Q.70 Ligands: SO4.20 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:R.73, F:D.76

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: N.159 Ligands: GOL.14 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain A: E.135, E.152, R.153, W.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.135, A:R.153, A:W.154 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain A: N.159 Chain B: K.72 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159 GOL.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.21: 1 residues within 4Å: Ligands: GOL.22 No protein-ligand interaction detected (PLIP) GOL.22: 1 residues within 4Å: Ligands: GOL.21 No protein-ligand interaction detected (PLIP) GOL.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.25: 1 residues within 4Å: Chain G: X.8 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
D

F
F

E
E

G
G

Rabphilin-3A

Synaptosomal-associated protein 25

Synaptosomal-associated protein 25

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