SMTL ID : 4h03.1

Crystal structure of NAD+-Ia-actin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: Y.256, R.300, R.301, G.303, Q.305, E.306, Y.338, P.339, N.340, S.343, T.344, F.354, R.357, E.383, E.385 Ligands: EDO.3, EDO.8, EDO.20, EDO.32 20 PLIP interactions: 20 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:E.306, A:N.340, A:N.340, A:S.343, A:R.357, A:E.383, A:E.385 Water bridges: A:R.300, A:F.341, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.28, A:D.91 Salt bridges: A:R.10

48 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: 8 residues within 4Å: Chain A: Y.65, D.66, Y.67, M.351, S.352 Chain B: M.176, N.280, K.284 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: D.400, S.401 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: A.106, N.108, T.130, K.328, E.332 Ligands: EDO.16 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: E.306, I.336, T.337, Y.338 Ligands: NAD.1 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: I.85, T.169, G.170, I.184, E.185, D.187 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: I.22, Y.147, D.179, V.180 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: K.16, K.18, Y.147, E.148, P.149, G.150, D.153 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: K.367, D.368 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: Y.47, K.48, S.51, D.143, Y.174, N.176, K.181 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: F.64, K.403, D.404, G.405 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: K.137, Q.138, D.139, D.187, Y.188, D.217, I.297, R.362 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: A.106, F.107, N.108, K.109 Ligands: EDO.7 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain A: R.112, E.114, K.155, P.156, T.157, P.158, K.203, Y.205 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: N.95, H.162, K.164, E.209, A.210 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: L.311, S.313, P.314, Y.316, D.317, K.358 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: Y.251, Y.256, N.260, R.300, F.341, I.342, S.343, L.387 Ligands: NAD.1 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.55, Q.59, D.139, F.141, K.142, Q.186 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: A.353, R.357 Chain B: M.269, E.270 Ligands: EDO.32 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: S.215, L.216, D.217, K.224 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: D.66, I.69, E.70, D.220 Ligands: EDO.25 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: E.70, E.75, K.79 Ligands: EDO.24 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: H.73, D.157, G.158, D.179, R.183, D.184 Ligands: EDO.30 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: Y.69, R.183, R.206 Ligands: EDO.29 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: Y.188, K.191, I.267 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: G.303, P.304, Q.305, R.357 Chain B: G.268, E.270 Ligands: NAD.1, EDO.22 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain B: S.141, L.142, S.145, V.298, M.299, P.332, R.335, S.338 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: Y.279, M.283, R.290, Y.294, P.322, M.325 Ligands: EDO.52 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: T.318, A.321, P.322, S.323, M.325, I.327 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain B: S.145, G.146 Ligands: EDO.37 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: S.145, R.147 Ligands: EDO.36 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: R.147, T.148, T.149, N.296 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: Y.166, D.288, D.292 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: L.171, H.173, K.284, C.285, D.286 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: E.83, H.87, F.127 Ligands: EDO.42 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: Y.91, E.99, T.126, F.127 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: I.208, L.242, P.243, D.244 Ligands: EDO.44 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain B: Y.198, S.199, F.200, E.205, L.242, Q.246 Ligands: EDO.43 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain B: R.210, D.211, E.214 Ligands: LAR.28 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain B: R.196, A.230, S.233, E.237, G.251, N.252 Ligand excluded by PLIP EDO.47: 9 residues within 4Å: Chain B: K.213, E.214, K.215, L.216, C.217, M.305, Y.306, P.307 Ligands: ATP.27 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain B: F.262, Q.263, H.275, R.312, E.316 Ligands: EDO.50 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain B: Q.263, P.264, S.265 Ligands: EDO.50 Ligand excluded by PLIP EDO.50: 9 residues within 4Å: Chain A: K.356 Chain B: F.262, Q.263, A.272, G.273, H.275, E.276 Ligands: EDO.48, EDO.49 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain A: Y.67, S.71 Chain B: Y.279, M.283 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain B: Y.279, M.283, L.320, A.321, P.322 Ligands: EDO.34 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain A: E.70, S.71 Chain B: R.290 Ligand excluded by PLIP

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

CA.26: 1 residues within 4Å: Ligands: ATP.27 No protein-ligand interaction detected (PLIP)

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

ATP.27: 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.26, LAR.28, EDO.47 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: 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:K.18, B:K.18, B:D.154, 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.28: 18 residues within 4Å: Chain B: G.15, L.16, P.32, I.34, D.56, Q.59, L.67, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Ligands: ATP.27, EDO.45 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.32, B:I.34, B:I.34, B:Q.59, B:L.67, 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

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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