SMTL ID : 5mzn.1

Helicase Sen1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: K.243, L.244, N.245, Q.248, G.269, T.270, G.271, K.272, T.273, K.274, R.331, Y.500, R.501 Ligands: EDO.8, EDO.12, MG.65 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:N.245, A:N.245, A:Q.248, A:Q.248, A:T.270, A:G.271, A:K.272, A:T.273, A:T.273, A:K.274, A:K.274 Water bridges: A:G.269, A:G.269, A:G.269, A:K.272, A:T.273, A:R.331, A:R.331, A:R.331, A:R.331, A:E.436 Salt bridges: A:K.272, A:R.331 pi-Stacking: A:Y.500, A:Y.500 pi-Cation interactions: A:K.274, A:K.274

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

EDO.2: 6 residues within 4Å: Chain A: S.511, L.519, K.520, D.521 Ligands: EDO.15, PEG.64 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: T.198, R.202, G.352, T.413, S.415, G.416, H.419 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: D.21, N.23, P.24, S.101, F.103 Ligands: EDO.39 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: S.38, E.39, W.75, Q.76, C.79, R.82, D.83 Ligands: EDO.11, PEG.59 Ligand excluded by PLIP EDO.6: 10 residues within 4Å: Chain A: R.36, S.38, Y.40, D.42, D.43, E.44, P.45, I.46, Y.49 Ligands: EDO.17 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.41, D.42, E.44, N.48, Y.49, P.68 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Y.242, K.243, K.274 Ligands: ADP.1, EDO.12 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.568, I.571, E.572, R.610, Y.611, S.703 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: F.652, L.653, F.656 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: E.39, Q.76, L.470, S.471, G.472, A.473 Ligands: EDO.5, EDO.25, EDO.35 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: K.243, L.244, N.245, Y.500 Ligands: ADP.1, EDO.8, EDO.16 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: P.227, S.492, P.493, Y.494, L.495 Ligands: EDO.37 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: K.274, L.277, R.331 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: N.245, V.498, Y.500, K.520, D.521, G.522, P.523 Ligands: EDO.2, EDO.16 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: K.239, L.244, N.245, T.246, V.498, Y.500 Ligands: EDO.12, EDO.15 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: R.36, N.37, S.38, E.39, Y.40, D.43 Ligands: EDO.6 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: N.322, A.323, D.326, S.354, D.355, V.356 Ligands: PEG.54 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: L.332, K.333, G.335, F.344, K.345, P.346, L.348, L.364 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: K.16, V.20, G.209, Y.212 Ligands: EDO.21, EDO.38, PEG.55 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: E.211, Y.212 Ligands: EDO.20, EDO.38, GOL.44, PEG.55 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: P.59, V.216, G.217, L.220 Ligands: EDO.30, GOL.45 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: L.366, E.367, V.370, R.396, R.397, Q.400 Ligands: PEG.60 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: E.436, Q.439, Q.464, Q.629, G.630 Ligands: PEG.57 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: E.39, Y.40, G.472, A.473, N.476 Ligands: EDO.11, EDO.35 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: P.45, I.46, G.47, N.48 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain A: P.466, S.475, N.476, K.478, N.480, Q.481, L.653, R.657 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: D.497, R.518, K.520 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain A: I.547, I.548, S.549, N.563, E.565, E.566, V.641, G.674, H.675 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain A: F.55, F.56, N.57, S.58, G.217, L.220, Q.221 Ligands: EDO.22 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: P.89, F.90, S.91, F.134, L.140, Y.190 Ligands: EDO.32, PEG.56 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: S.91, I.92, I.93, S.109, V.110, E.188 Ligands: EDO.31, PEG.56 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: Q.535, L.536, E.537 Ligands: EDO.34, GOL.48 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: E.537, P.538, Y.576, L.706, P.708 Ligands: EDO.33 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain A: V.469, L.470, S.471, G.472, S.475 Ligands: EDO.11, EDO.25 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: P.132, D.133, F.134, R.135, Y.190 Ligand excluded by PLIP EDO.37: 11 residues within 4Å: Chain A: P.224, S.225, K.258, F.261, S.262, L.263, S.491, S.492, P.493, Y.494 Ligands: EDO.13 Ligand excluded by PLIP EDO.38: 9 residues within 4Å: Chain A: V.20, Q.63, E.208, G.209, E.211, Y.212 Ligands: EDO.20, EDO.21, PEG.55 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain A: N.23, P.24, E.27, S.101, D.102, F.103 Ligands: EDO.4 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain A: N.490, S.491, S.492 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain A: T.162, D.168 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.42: 6 residues within 4Å: Chain A: P.504, S.505, K.508, R.695, C.697 Ligands: PEG.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.695, A:R.695 Water bridges: A:S.505 GOL.43: 4 residues within 4Å: Chain A: Y.561, Y.597, R.598, E.599 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.561, A:R.598, A:E.599 GOL.44: 3 residues within 4Å: Chain A: P.59, E.211 Ligands: EDO.21 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.211, A:E.211, A:E.211, A:E.211, A:E.211 GOL.45: 6 residues within 4Å: Chain A: D.214, L.215, V.216, G.217, Q.218 Ligands: EDO.22 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.214, A:D.214, A:G.217, A:Q.218, A:Q.218 Water bridges: A:D.214 GOL.46: 7 residues within 4Å: Chain A: E.259, F.283, K.287, Q.313, D.430, T.431, R.455 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.287, A:Q.313, A:Q.313, A:R.455, A:R.455 Water bridges: A:E.259, A:K.287, A:D.430 GOL.47: 5 residues within 4Å: Chain A: P.523, G.524, M.525, I.527, L.528 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.524, A:L.528 Water bridges: A:P.523 GOL.48: 4 residues within 4Å: Chain A: H.534, Q.535, E.537 Ligands: EDO.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.534, A:E.537, A:E.537 GOL.49: 3 residues within 4Å: Chain A: K.693, D.694, S.696 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.693, A:D.694, A:S.696 GOL.50: 4 residues within 4Å: Chain A: L.698, A.699, Y.700, F.720 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.698, A:Y.700, A:F.720 Water bridges: A:S.696, A:L.698, A:L.698 GOL.51: 6 residues within 4Å: Chain A: D.371, I.374, N.378, Y.379, R.392, R.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.379, A:R.396 GOL.52: 3 residues within 4Å: Chain A: R.97, T.98, A.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:A.99 GOL.53: 6 residues within 4Å: Chain A: M.195, Q.196, M.197, T.198, T.199, I.200 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.196, A:Q.196, A:T.198, A:T.199, A:T.199 Water bridges: A:K.193, A:Q.196, A:T.198

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.54: 10 residues within 4Å: Chain A: D.326, L.330, R.353, S.354, V.356, V.357, N.358, I.361, K.362 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.358, A:N.358 PEG.55: 6 residues within 4Å: Chain A: Q.63, K.67, E.208 Ligands: EDO.20, EDO.21, EDO.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.67 Water bridges: A:Q.63, A:E.208, A:E.208 PEG.56: 11 residues within 4Å: Chain A: F.90, S.91, I.92, I.93, S.109, V.110, A.111, V.114, N.166 Ligands: EDO.31, EDO.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:A.111 PEG.57: 10 residues within 4Å: Chain A: P.268, G.269, Q.464, R.501, Q.629, G.630, Q.631, E.632, R.665 Ligands: EDO.24 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.464, A:E.632, A:R.665, A:R.665 Water bridges: A:K.272, A:E.436, A:G.630 PEG.58: 7 residues within 4Å: Chain A: R.82, D.83, R.84, D.86, S.141, S.142, D.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.83, A:D.86 Water bridges: A:S.142 PEG.59: 8 residues within 4Å: Chain A: T.35, R.36, N.37, S.38, R.82, D.83, K.146 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.82, A:K.146 Water bridges: A:N.37 PEG.60: 7 residues within 4Å: Chain A: R.353, K.362, E.367, E.368, D.371, R.396 Ligands: EDO.23 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.353, A:R.353, A:E.367, A:E.367, A:E.368, A:E.368 Water bridges: A:R.396 PEG.61: 5 residues within 4Å: Chain A: A.401, H.402, A.405, M.425 Ligands: PEG.62 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.425 PEG.62: 3 residues within 4Å: Chain A: H.402, V.406 Ligands: PEG.61 No protein-ligand interaction detected (PLIP) PEG.63: 4 residues within 4Å: Chain A: K.508, D.691, R.695 Ligands: GOL.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.508 PEG.64: 7 residues within 4Å: Chain A: S.511, G.517, R.518, L.519, K.520, D.521 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.511

1 x MG: MAGNESIUM ION(Non-covalent)

MG.65: 3 residues within 4Å: Chain A: K.272, T.273 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.273, H2O.8, H2O.8, H2O.11, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leonaite, B. et al., Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. EMBO J. (2017)

Release Date

2017-04-19

Peptides

Helicase SEN1,Helicase SEN1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Helicase SEN1,Helicase SEN1

Related Entries With Identical Sequence