SMTL ID : 6lyo.1

Crystal Structure of H296A mutant of Formylglycinamidine Synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: V.342, F.344, T.395, G.396, Y.397, F.398, K.658, L.661, V.662, Q.677, P.685, A.687, D.688, E.727, N.731, D.893, S.895 Ligands: MG.61, MG.62, MG.63 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.395, A:G.396, A:Y.397, A:Y.397, A:Q.677, A:A.687, A:D.688, A:N.731, A:S.895 Water bridges: A:K.658, A:K.658, A:K.658, A:D.896, A:D.896, A:D.896 Salt bridges: A:K.658

37 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.718, R.722, D.764, K.767, E.772 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: E.657, T.659, M.678, W.682, Q.683, R.991, E.1014, K.1018, R.1177 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: H.911, C.912, A.969, G.970, R.987, D.1021 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: A.920, V.961, H.962, Y.963 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: K.1237, V.1238, T.1239, E.1240 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: V.441, T.590, E.591, E.592 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: Q.776, D.868, V.869, A.870 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: E.273, S.275, A.276, P.295, H.297 Ligands: GOL.37 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: H.162, Q.163 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: P.1136, N.1260, R.1262 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: A.752, A.753, G.754, H.755, P.756, K.791, R.793, E.802 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: D.259, Y.260, E.273 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: E.1182, T.1184, Q.1185, R.1230 Ligands: GOL.22 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: P.88, S.94, W.96, E.116, R.117 Ligands: GOL.30 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: Q.356, P.357, W.358, K.647, R.648, H.651 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: R.489, K.577, R.580, A.581, P.582 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: G.922, D.923, D.924 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: R.24, W.314, E.377, L.380, R.1005, R.1173 Ligand excluded by PLIP GOL.20: 1 residues within 4Å: Chain A: H.844 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: V.625, Q.626, H.755, P.756, G.757, D.759 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: E.1222, R.1230, V.1238, N.1251 Ligands: GOL.14 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain A: K.444, D.538, V.585, I.586, G.587, D.588 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain A: H.307, K.418, S.789 Ligands: SO4.59 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: R.1154, W.1163, R.1165, R.1213, H.1217 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain A: K.647, E.985, W.993 Ligands: GOL.32 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain A: Y.46, V.119 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: P.95, M.145, W.314, P.315, R.481, D.482 Ligands: GOL.30 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: H.228, K.301, E.303, G.784, K.785 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain A: P.88, S.94, P.95, E.146 Ligands: GOL.15, GOL.28 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain A: E.201, K.205 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain A: V.992, W.993, E.996 Ligands: GOL.26 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain A: E.1130, H.1134, R.1154, E.1155, L.1156, I.1157, P.1158 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain A: Y.699, R.821, V.1277, W.1286, G.1287, E.1288 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain A: N.57, D.58 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain A: P.72, A.73, L.74, R.1209, E.1211 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain A: E.273, P.295 Ligands: GOL.9 Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain A: A.958, D.959 Ligand excluded by PLIP

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

EDO.38: 2 residues within 4Å: Chain A: R.945, Y.963 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.945, A:R.945 EDO.40: 4 residues within 4Å: Chain A: Q.38, V.39, H.40, S.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.126, A:S.126

20 x SO4: SULFATE ION(Non-functional Binders)

SO4.41: 6 residues within 4Å: Chain A: H.225, T.304, A.305, N.306, H.307, S.787 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain A: H.1095, R.1135, P.1136, Q.1137, T.1138 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain A: W.314, R.1168, R.1173 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain A: G.1236, K.1237, V.1238 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain A: P.1049, K.1050, N.1093, H.1095 Ligand excluded by PLIP SO4.46: 6 residues within 4Å: Chain A: S.21, A.22, F.23, N.1007, Q.1009, H.1170 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain A: Q.1185, Q.1192, G.1193, M.1194, V.1195 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain A: N.1122, R.1124 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain A: P.365, E.366, R.367, W.794 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain A: T.641, I.642 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain A: H.225, E.303, G.513, A.514, K.785 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain A: K.842, H.844, R.867 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain A: S.76, H.77, T.78 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain A: L.187, Y.216, L.457, E.550 Ligand excluded by PLIP SO4.55: 4 residues within 4Å: Chain A: Q.63, L.1120, F.1121, H.1123 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain A: R.227, N.232, T.618, K.620 Ligand excluded by PLIP SO4.57: 1 residues within 4Å: Chain A: R.1003 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain A: P.1041, Y.1042 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain A: H.225, H.307, S.789 Ligands: GOL.24 Ligand excluded by PLIP SO4.60: 6 residues within 4Å: Chain A: P.357, D.639, R.648, V.855, Y.856, R.857 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.61: 4 residues within 4Å: Chain A: D.688, N.731, D.893 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.688, A:D.893, H2O.5, H2O.22 MG.62: 2 residues within 4Å: Chain A: E.727 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.727, H2O.6, H2O.6, H2O.12, H2O.14 MG.63: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, N. et al., Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. Acs Catalysis (2022)

Release Date

2021-02-17

Peptides

Phosphoribosylformylglycinamidine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoribosylformylglycinamidine synthase