SMTL ID : 4h0x.1

Crystal structure of NAD+-Ia(E380A)-actin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 17 residues within 4Å: Chain A: Y.256, I.264, R.300, R.301, G.303, Q.305, E.306, Y.338, P.339, N.340, S.343, T.344, S.345, F.354, R.357, E.383 Ligands: EDO.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.256, A:Y.256, A:R.301, A:R.301, A:G.303, A:G.303, A:Q.305, A:Q.305, A:E.306, A:N.340, A:N.340, A:S.343, A:R.357 Salt bridges: A:R.300, A:R.300, A:R.357

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

PO4.2: 5 residues within 4Å: Chain A: R.10, W.24, E.28, I.90, D.91 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.28, A:D.91, A:D.91, A:K.92 Salt bridges: A:R.10

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

EDO.3: 8 residues within 4Å: Chain A: Y.299, R.301, S.345, G.347, S.348, V.349, F.354 Ligands: NAD.1 Ligand excluded by PLIP EDO.4: 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.5: 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.6: 6 residues within 4Å: Chain A: I.85, T.169, G.170, I.184, E.185, D.187 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: 5 residues within 4Å: Chain A: N.95, H.162, K.164, E.209, A.210 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: K.164, S.211, I.212 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: K.137, D.187, Y.188, S.189, S.215, I.297 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: H.73, G.158, D.179, D.184 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: R.183, R.206 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 9 residues within 4Å: Chain B: S.141, L.142, S.145, V.298, M.299, S.300, P.332, R.335, S.338 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: M.283, R.290, Y.294, P.322 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: T.318, A.321, P.322, S.323, M.325, I.327 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.147, T.148, T.149, N.296 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: Y.166, D.288, D.292 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: E.83, K.84, H.87, F.127 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: Y.91, P.98, E.99, T.126, F.127 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: Y.198, S.199, F.200, E.205, L.242 Ligand excluded by PLIP EDO.25: 9 residues within 4Å: Chain B: K.213, E.214, K.215, L.216, C.217, M.305, Y.306, P.307 Ligands: ATP.13 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: Q.263, P.264, S.265 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: K.356 Chain B: F.262, A.272, G.273, H.275, E.276 Ligands: EDO.26 Ligand excluded by PLIP

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

CA.12: 1 residues within 4Å: Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

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

ATP.13: 23 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.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.12, LAR.14, EDO.25 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:G.15, B:L.16, B:G.156, B:D.157, B:D.157, B:D.157, B:G.158, B:V.159, B:V.159, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303, B:K.336 Water bridges: B:D.11, B:K.18, B:K.18, B:Q.137, B:D.154, B:D.154, B:V.159, B:Y.306, B:K.336 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306

1 x LAR: LATRUNCULIN A(Non-covalent)

LAR.14: 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.13 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.32, B:I.34, B:I.34, B:E.207 Hydrogen bonds: B:Y.69, B:D.157, B:T.186, B:E.207, B:R.210, B:K.213 Salt bridges: B:R.210

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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