SMTL ID : 6i59.1

Long wavelength native-SAD phasing of Sen1 helicase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

monomer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: K.243, L.244, N.245, Q.248, T.270, G.271, K.272, T.273, K.274, E.327, R.331, Y.500 Ligands: EDO.8, EDO.12, MG.65 19 PLIP interactions: 19 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:K.274 Water bridges: A:G.269, A:K.272, A:R.331, A:R.331 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: 3 residues within 4Å: Chain A: K.520, D.521 Ligands: PEG.64 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: R.202, G.416, H.419 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: D.21, N.23 Ligands: EDO.39 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: S.38, E.39, Q.76 Ligands: EDO.11, PEG.59 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: R.36, Y.40, D.42, D.43, E.44 Ligands: EDO.17 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: D.42, E.44, N.48, Y.49, P.68 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.243, K.274 Ligands: ADP.1, EDO.12 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: R.568, E.572, Y.611 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: F.652, F.656 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: E.39, Q.76, L.470, S.471, G.472 Ligands: EDO.5, EDO.35 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: K.243, L.244, N.245 Ligands: ADP.1, EDO.8, EDO.16 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.492, P.493, Y.494 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: 5 residues within 4Å: Chain A: V.498, K.520, D.521, P.523 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.239, N.245, T.246 Ligands: EDO.12, EDO.15 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: R.36, N.37, S.38, D.43 Ligands: EDO.6 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: N.322, A.323, D.326, V.356 Ligands: PEG.54 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: L.332, K.345, P.346, L.348 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: K.16, Y.212 Ligands: EDO.38 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: E.211 Ligands: EDO.38, GOL.44, PEG.55 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: P.59, V.216, L.220 Ligands: EDO.30 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: L.366, E.367, R.396, Q.400 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: 3 residues within 4Å: Chain A: E.39, G.472, N.476 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: P.45, I.46, G.47 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: S.475, K.478, N.480, 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: 7 residues within 4Å: Chain A: I.547, S.549, N.563, E.565, E.566, V.641, H.675 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: F.55, F.56, N.57, L.220, Q.221 Ligands: EDO.22 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain A: S.91, L.140 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: S.91, I.92, I.93, S.109, E.188 Ligands: PEG.56 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: Q.535, L.536, E.537 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: E.537, Y.576, L.706, P.708 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: V.469, L.470, G.472 Ligands: EDO.11 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain A: P.132, F.134 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain A: P.224, K.258, S.262, L.263, S.491, S.492, P.493, Y.494 Ligands: EDO.13 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain A: E.208, G.209, E.211 Ligands: EDO.20, EDO.21, PEG.55 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain A: N.23, E.27, S.101, D.102, F.103 Ligands: EDO.4 Ligand excluded by PLIP EDO.40: 1 residues within 4Å: Chain A: N.490 Ligand excluded by PLIP EDO.41: 1 residues within 4Å: Chain A: D.168 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.42: 3 residues within 4Å: Chain A: S.505, R.695 Ligands: PEG.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.505, 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: 2 residues within 4Å: Chain A: E.211 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.211 GOL.45: 5 residues within 4Å: Chain A: D.214, L.215, V.216, G.217, Q.218 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.216, A:G.217, A:Q.218, A:Q.218 Water bridges: A:D.214 GOL.46: 5 residues within 4Å: Chain A: E.259, K.287, Q.313, D.430, R.455 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.259, A:E.259, A:K.287, A:Q.313, A:Q.313, A:R.455, A:R.455 Water bridges: A:V.256, A:K.287 GOL.47: 4 residues within 4Å: Chain A: P.523, G.524, I.527, L.528 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.528 Water bridges: A:P.523 GOL.48: 3 residues within 4Å: Chain A: H.534, Q.535, E.537 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.537, A:E.537 Water bridges: A:H.534 GOL.49: 3 residues within 4Å: Chain A: K.693, D.694, S.696 2 PLIP interactions: 2 interactions with chain A Water bridges: 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: 5 residues within 4Å: Chain A: D.371, I.374, Y.379, R.392, R.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.379, A:R.396 Water bridges: A:D.371, A:Y.379 GOL.52: 2 residues within 4Å: Chain A: T.98, A.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.99 GOL.53: 4 residues within 4Å: Chain A: Q.196, M.197, T.198, T.199 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.198, A:T.199, A:T.199, A:T.199 Water bridges: A:Q.196, A:Q.196

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

PEG.54: 7 residues within 4Å: Chain A: D.326, S.354, V.356, V.357, N.358, I.361 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.326, A:S.354, A:N.358 PEG.55: 5 residues within 4Å: Chain A: Q.63, K.67, E.208 Ligands: EDO.21, EDO.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.67 Water bridges: A:Q.63, A:K.67 PEG.56: 5 residues within 4Å: Chain A: S.91, V.110, A.111, V.114 Ligands: EDO.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.91, A:S.91, A:A.111 PEG.57: 8 residues within 4Å: Chain A: P.268, Q.464, R.501, Q.629, G.630, E.632, R.665 Ligands: EDO.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.464, A:Q.629, A:G.630, A:R.665 PEG.58: 4 residues within 4Å: Chain A: R.82, D.83, D.86, S.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:S.142 Water bridges: A:S.142 PEG.59: 7 residues within 4Å: Chain A: T.35, R.36, N.37, R.82, D.83, K.146 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.37, A:K.146 PEG.60: 5 residues within 4Å: Chain A: R.353, K.362, E.367, E.368, D.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.353, A:R.353, A:E.367, A:E.368 PEG.61: 4 residues within 4Å: Chain A: A.401, H.402, A.405 Ligands: PEG.62 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.311 PEG.62: 1 residues within 4Å: Ligands: PEG.61 No protein-ligand interaction detected (PLIP) PEG.63: 2 residues within 4Å: Chain A: K.508 Ligands: GOL.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.508 Water bridges: A:K.508, A:D.691 PEG.64: 5 residues within 4Å: Chain A: G.517, R.518, L.519, K.520 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.519 Water bridges: A:S.511

1 x MG: MAGNESIUM ION(Non-covalent)

MG.65: 3 residues within 4Å: Chain A: T.273, D.435 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.273, H2O.3, H2O.6, H2O.11, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basu, S. et al., Long-wavelength native-SAD phasing: opportunities and challenges. Iucrj (2019)

Release Date

2019-03-13

Peptides

Helicase SEN1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Helicase SEN1

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