SMTL ID : 2p0a.1

The crystal structure of human synapsin III (SYN3) in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: S.97, M.98, A.99, L.100, A.179, H.180 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: S.97, M.98, A.99, L.100, A.179, H.180 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain C: S.97, M.98, A.99, L.100, A.179, H.180 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain D: S.97, M.98, A.99, L.100, A.179, H.180 Ligand excluded by PLIP

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

SO4.2: 6 residues within 4Å: Chain A: A.27, R.92, P.299, L.300, R.309 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.300 Water bridges: A:D.25, A:R.92, A:R.92 Salt bridges: A:R.92, A:R.309 SO4.3: 8 residues within 4Å: Chain A: R.221, R.234, N.244, K.279, M.294, P.299, I.301 Ligands: ANP.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.244 Water bridges: A:R.234, A:R.234 Salt bridges: A:R.221, A:R.234, A:K.279 SO4.4: 5 residues within 4Å: Chain A: E.303, H.304, V.305, E.306, E.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.304, A:E.306, A:E.307, A:E.307 Salt bridges: A:H.304 SO4.5: 3 residues within 4Å: Chain A: Y.96, R.105 Chain B: R.105 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.103, A:D.103 Water bridges: A:Y.96, A:Y.96, A:R.105, A:R.105, B:Y.96, B:D.103, B:D.103, B:R.105 Salt bridges: A:R.105, B:R.105 SO4.13: 5 residues within 4Å: Chain B: A.27, R.92, P.299, L.300, R.309 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.300 Water bridges: B:D.25, B:R.92 Salt bridges: B:R.92, B:R.309 SO4.14: 8 residues within 4Å: Chain B: R.221, R.234, N.244, K.279, M.294, P.299, I.301 Ligands: ANP.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.244 Salt bridges: B:R.221, B:R.234, B:K.279 SO4.20: 6 residues within 4Å: Chain C: A.27, R.92, P.299, L.300, R.309 Ligands: EDO.27 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.300 Water bridges: C:D.25, C:R.92, C:R.92 Salt bridges: C:R.92, C:R.309 SO4.21: 8 residues within 4Å: Chain C: R.221, R.234, N.244, K.279, M.294, P.299, I.301 Ligands: ANP.24 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.244 Water bridges: C:R.234, C:R.234 Salt bridges: C:R.221, C:R.234, C:K.279 SO4.22: 5 residues within 4Å: Chain C: E.303, H.304, V.305, E.306, E.307 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.304, C:E.306, C:E.307 Salt bridges: C:H.304 SO4.23: 3 residues within 4Å: Chain C: Y.96, R.105 Chain D: R.105 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C Water bridges: D:D.103, D:R.105, D:R.105, C:Y.96, C:R.105, C:R.105, C:R.105 Salt bridges: D:R.105, C:R.105 Hydrogen bonds: C:D.103 SO4.31: 5 residues within 4Å: Chain D: A.27, R.92, P.299, L.300, R.309 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.300 Water bridges: D:D.25, D:R.92 Salt bridges: D:R.92, D:R.309 SO4.32: 8 residues within 4Å: Chain D: R.221, R.234, N.244, K.279, M.294, P.299, I.301 Ligands: ANP.33 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.244 Salt bridges: D:R.221, D:R.234, D:K.279

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 22 residues within 4Å: Chain A: K.131, V.173, K.175, A.179, H.180, A.181, G.182, K.185, E.211, A.212, F.213, I.214, D.219, W.241, K.242, A.243, N.244, K.279, V.281, I.291, E.292 Ligands: SO4.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.131, A:K.175, A:A.181, A:G.182, A:K.185, A:E.211, A:E.211, A:I.214, A:D.219, A:A.243, A:N.244, A:K.279, A:K.279, A:K.279 Water bridges: A:H.94, A:E.292 Salt bridges: A:K.131, A:K.175, A:K.185, A:K.279 ANP.15: 23 residues within 4Å: Chain B: K.131, V.173, K.175, A.179, H.180, A.181, G.182, K.185, E.211, A.212, F.213, I.214, D.219, R.234, W.241, K.242, A.243, N.244, K.279, V.281, I.291, E.292 Ligands: SO4.14 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:K.131, B:K.175, B:A.181, B:G.182, B:K.185, B:E.211, B:I.214, B:D.219, B:R.234, B:A.243, B:N.244, B:N.244, B:K.279, B:K.279, B:K.279 Water bridges: B:H.94, B:H.180, B:E.292 Salt bridges: B:K.131, B:K.175, B:K.185, B:K.279 ANP.24: 22 residues within 4Å: Chain C: K.131, V.173, K.175, A.179, H.180, A.181, G.182, K.185, E.211, A.212, F.213, I.214, D.219, W.241, K.242, A.243, N.244, K.279, V.281, I.291, E.292 Ligands: SO4.21 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:K.131, C:K.175, C:H.180, C:A.181, C:G.182, C:K.185, C:E.211, C:I.214, C:D.219, C:A.243, C:N.244, C:K.279, C:K.279, C:K.279 Water bridges: C:H.94, C:D.219, C:E.292 Salt bridges: C:K.131, C:K.175, C:K.185, C:K.279 ANP.33: 23 residues within 4Å: Chain D: K.131, V.173, K.175, A.179, H.180, A.181, G.182, K.185, E.211, A.212, F.213, I.214, D.219, R.234, W.241, K.242, A.243, N.244, K.279, V.281, I.291, E.292 Ligands: SO4.32 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:K.131, D:K.175, D:H.180, D:A.181, D:G.182, D:K.185, D:E.211, D:E.211, D:I.214, D:D.219, D:R.234, D:A.243, D:N.244, D:N.244, D:K.279, D:K.279, D:K.279 Water bridges: D:H.94, D:D.219, D:E.292 Salt bridges: D:K.131, D:K.175, D:K.185, D:K.279

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: V.153, E.154, A.212, Y.289 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: I.186, K.187, V.188, E.189, D.193 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.92, H.94, S.297, P.299 Ligands: SO4.2 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: L.192, D.193, D.196 Chain D: I.186, K.187, W.241 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: F.142, P.147, P.151, L.152, E.154, Y.289 Ligands: EDO.7 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: F.142, P.147, P.151, L.152, E.154, Y.289 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: V.153, E.154, A.212, Y.289 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: Q.137, K.140 Chain B: Q.112, S.121, Y.123 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain C: V.153, E.154, A.212, Y.289 Ligands: EDO.29 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: I.186, K.187, V.188, E.189, D.193 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: R.92, H.94, S.297, P.299 Ligands: SO4.20 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: I.186, K.187, W.241 Chain C: L.192, D.193, D.196 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain C: F.142, P.147, P.151, L.152, E.154, Y.289 Ligands: EDO.25 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain D: F.142, P.147, P.151, L.152, E.154, Y.289 Ligands: EDO.35 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: V.153, E.154, A.212, Y.289 Ligands: EDO.34 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: Q.137, K.140 Chain D: Q.112, S.121, Y.123 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turnbull, A.P. et al., The crystal structure of human synapsin III (SYN3) in complex with AMPPNP. To be Published

Release Date

2007-03-27

Peptides

Synapsin-3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Synapsin-3