SMTL ID : 4h0t.1

Crystal structure of Ia-ADPR-actin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: R.10, W.24, E.28, I.90, D.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91 Water bridges: A:R.10, A:D.91 Salt bridges: A:R.10

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

EDO.2: 6 residues within 4Å: Chain A: Y.299, R.301, S.345, G.347, S.348, V.349 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: M.351, S.352, A.353 Chain B: I.175, M.176, R.177 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Y.65, D.66, M.351, S.352 Chain B: M.176, N.280, K.284 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: I.85, T.169, G.170, I.184, E.185, D.187 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: K.367, D.368 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: Y.47, S.51, D.143, Y.174, N.176, K.181 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: Y.65, Q.68, N.350, A.355, K.356, D.404 Chain B: E.276 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: R.112, E.114, K.155, P.156, P.158, K.203, Y.205 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: N.95, H.162, K.164, E.209, A.210 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: H.73, D.157, G.158, D.179, D.184 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: G.303, P.304, Q.305, L.311, R.357 Chain B: G.268, E.270 Ligands: AR6.11 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: S.141, S.145, V.298, M.299, S.300, P.332, R.335, S.338 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: Y.279, M.283, R.290, Y.294, P.322 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: Y.166, D.288, D.292 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Y.91, E.99, T.126, F.127 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: Y.198, S.199, F.200, E.205 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain B: K.213, E.214, K.215, L.216, C.217, M.305, Y.306, P.307 Ligands: ATP.14 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: K.356 Chain B: F.262, A.272, G.273, H.275, E.276 Ligand excluded by PLIP

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Covalent)

AR6.11: 15 residues within 4Å: Chain A: Y.256, I.264, R.300, G.303, Q.305, E.306, Y.338, N.340, F.354, R.357, A.381, G.382 Chain B: R.177, D.179 Ligands: EDO.16 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.256, A:G.303, A:Q.305, A:E.306, A:E.306, A:N.340, A:N.340, A:A.381, B:R.177 Salt bridges: A:R.300, A:R.300, A:R.357

1 x CA: CALCIUM ION(Non-functional Binders)

CA.12: 1 residues within 4Å: Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

1 x LAR: LATRUNCULIN A(Non-covalent)

LAR.13: 18 residues within 4Å: Chain B: G.15, L.16, P.32, I.34, D.56, Q.59, R.62, L.67, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Ligands: ATP.14 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.32, B:I.34, B:I.34, B:Q.59, B:E.207 Hydrogen bonds: B:Y.69, B:D.157, B:T.186, B:E.207, B:K.213 Salt bridges: B:R.210

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.14: 24 residues within 4Å: Chain B: G.13, S.14, G.15, L.16, K.18, G.74, G.156, D.157, G.158, V.159, G.182, R.183, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.12, LAR.13, EDO.22 31 PLIP interactions: 31 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:G.15, B:L.16, B:L.16, B:G.74, B:G.156, B:D.157, B:D.157, B:D.157, B:G.158, B:V.159, B:V.159, B:R.210, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303, B:K.336 Water bridges: B:K.18, B:K.18, B:K.18, B:Q.137, B:D.154, B:D.154, B:D.154, B:Y.306 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsurumura, T. et al., Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-20

Peptides

Iota toxin component Ia: A
Actin, alpha skeletal muscle: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iota toxin component Ia

Actin, alpha skeletal muscle

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