SMTL ID : 6lyl.1

Crystal structure of S1052D mutant of Formylglycinamidine synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: H.228, N.268, K.301, E.303, G.784, K.785 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: H.225, T.304, H.305, N.306, H.307, S.787 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: W.314, R.1168, R.1173 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: H.225, E.303, G.513, A.514, K.785 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: H.1095, R.1135, P.1136, Q.1137, T.1138 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: Y.699, R.821 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: Q.1185, Q.1192, G.1193, M.1194, V.1195 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: P.1049, K.1050, N.1093, H.1095 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: T.641, I.642 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: Q.776, D.868, V.869, A.870 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: K.842, H.844, R.867 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: S.21, A.22, F.23, N.1007, H.1170 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: N.1122, R.1124 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: H.77, T.78 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: A.920, V.961, H.962 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: V.441, T.590, E.591, E.592 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: K.647, W.993 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: H.161, H.162, Q.163 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: Q.63, L.1120, F.1121, H.1123 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: R.227, K.229, N.232, K.620 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain A: N.1260, R.1262 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain A: P.365, E.366, R.367, W.794 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain A: W.1281, P.1283, E.1284 Ligand excluded by PLIP

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

MG.5: 4 residues within 4Å: Chain A: D.688, N.731, D.893 Ligands: ADP.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.688, A:D.893, H2O.4, H2O.18 MG.6: 2 residues within 4Å: Chain A: E.727 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.727, H2O.2, H2O.6, H2O.9, H2O.11 MG.7: 1 residues within 4Å: Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

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

ADP.8: 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.5, MG.6, MG.7 15 PLIP interactions: 15 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: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

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 6 residues within 4Å: Chain A: H.911, C.912, A.969, G.970, R.987, D.1021 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.970, A:G.970, A:R.987, A:D.1021 Water bridges: A:D.1021 GOL.27: 9 residues within 4Å: Chain A: E.657, T.659, M.678, W.682, Q.683, R.991, E.1014, K.1018, R.1177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.659, A:R.991, A:K.1018, A:R.1177 GOL.28: 3 residues within 4Å: Chain A: S.698, Y.699, Y.700 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.699, A:Y.700 GOL.29: 3 residues within 4Å: Chain A: W.999, H.1015, E.1016 No protein-ligand interaction detected (PLIP) GOL.30: 6 residues within 4Å: Chain A: A.718, R.722, D.764, K.767, A.768, E.772 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.722, A:R.722, A:E.772 Water bridges: A:E.772 GOL.31: 4 residues within 4Å: Chain A: A.634, L.635, R.637, D.861 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.635, A:R.637, A:D.861 Water bridges: A:R.637, A:L.847, A:L.847, A:G.848 GOL.32: 3 residues within 4Å: Chain A: G.922, D.923, D.924 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.923, A:D.923, A:D.924 Water bridges: A:N.845, A:N.845, A:D.924 GOL.33: 4 residues within 4Å: Chain A: E.273, A.276, P.295, H.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.273, A:E.273, A:A.276 Water bridges: A:A.276 GOL.34: 6 residues within 4Å: Chain A: G.754, H.755, P.756, K.791, R.793, E.802 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.793, A:E.802

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

EDO.37: 2 residues within 4Å: Chain A: T.641, A.643 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.643 EDO.38: 2 residues within 4Å: Chain A: H.844, K.862 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.862, A:K.862

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