SMTL ID : 6lyk.1

Crystal Structure of R1263A mutant of Formylglycinamidine Synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: R.1155, W.1164, R.1166, R.1214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1155 Water bridges: A:E.1212, A:R.1214, A:H.1218 EDO.2: 2 residues within 4Å: Chain A: R.946, Y.964 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.946, A:R.946 EDO.3: 4 residues within 4Å: Chain A: R.676, S.1281, W.1282, H.1283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.676, A:W.1282, A:H.1283 Water bridges: A:R.676, A:T.824 EDO.4: 5 residues within 4Å: Chain A: R.490, K.578, R.581, A.582, P.583 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.490 Water bridges: A:K.578 EDO.5: 4 residues within 4Å: Chain A: F.248, Y.266, V.784, G.785 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.785 Water bridges: A:P.783 EDO.6: 2 residues within 4Å: Chain A: R.822, H.823 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.823, A:R.887 EDO.7: 1 residues within 4Å: Chain A: T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.257 EDO.8: 3 residues within 4Å: Chain A: W.1282, P.1284, E.1285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1285 Water bridges: A:N.1286 EDO.9: 2 residues within 4Å: Chain A: N.58, D.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.59, A:D.59 Water bridges: A:S.60 EDO.10: 4 residues within 4Å: Chain A: P.314, V.370, D.374, E.378 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.313, A:E.378 EDO.12: 4 residues within 4Å: Chain A: P.73, A.74, R.1210, E.1212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.74, A:R.1210, A:R.1210, A:E.1212 EDO.13: 7 residues within 4Å: Chain A: P.19, L.21, I.26, Y.44, L.75, S.76, H.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.76 Water bridges: A:I.43, A:A.45 EDO.14: 3 residues within 4Å: Chain A: E.1260, N.1261 Ligands: SO4.37 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.1260, A:E.1260 EDO.15: 3 residues within 4Å: Chain A: R.67, R.1155, E.1156 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.67, A:R.67, A:N.1153, A:R.1155, A:R.1155, A:E.1156, A:E.1156 EDO.16: 3 residues within 4Å: Chain A: E.360, E.361, R.858 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.361, A:R.858 Water bridges: A:E.360, A:D.362

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 3 residues within 4Å: Chain A: R.228, N.233, K.621 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.622

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

ADP.17: 19 residues within 4Å: Chain A: V.343, F.345, T.396, G.397, Y.398, F.399, K.659, L.662, V.663, Q.678, P.686, A.688, D.689, E.728, N.732, S.896 Ligands: MG.19, MG.20, MG.21 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.396, A:T.396, A:G.397, A:Y.398, A:Q.678, A:A.688, A:N.732, A:S.896 Water bridges: A:T.396, A:T.655, A:K.659, A:K.659, A:K.659, A:D.897, A:D.897, A:D.897 Salt bridges: A:K.659

1 x GLN: GLUTAMINE(Non-covalent)

GLN.18: 13 residues within 4Å: Chain A: G.1102, G.1103, F.1104, D.1108, C.1145, N.1146, Q.1149, F.1175, S.1205, H.1206, G.1207, E.1208, H.1270 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.1103, A:D.1108, A:N.1146, A:Q.1149, A:G.1207, A:E.1208, A:H.1270, Q.18, Q.18 Water bridges: A:D.1108, A:S.1205

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

MG.19: 2 residues within 4Å: Chain A: E.728 Ligands: ADP.17 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.728, H2O.7, H2O.11, H2O.19, H2O.24 MG.20: 1 residues within 4Å: Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain A: D.689, N.732, D.894 Ligands: ADP.17 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.689, A:D.894, H2O.15, H2O.29 MG.22: 1 residues within 4Å: Chain A: T.1023 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1023

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

SO4.23: 6 residues within 4Å: Chain A: H.226, T.305, H.306, N.307, H.308, S.788 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain A: H.1096, R.1136, P.1137, Q.1138, T.1139 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain A: W.315, R.1169, R.1174 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain A: Y.700, R.822 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain A: P.366, E.367, R.368 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: P.1050, K.1051, N.1094, H.1096 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain A: S.22, A.23, F.24, N.1008, Q.1010, H.1171 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain A: N.1123, R.1125 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain A: T.642, I.643 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain A: Q.1186, Q.1193, G.1194, M.1195, V.1196 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain A: H.226, N.269, G.514, A.515, K.786 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain A: K.843, H.845, R.868 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain A: Q.64, L.1121, F.1122, H.1124 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain A: H.78, T.79 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain A: N.1261, R.1263 Ligands: EDO.14 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain A: H.162, H.163, Q.164 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain A: R.7, G.8, I.161, H.162 Ligand excluded by PLIP

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.40: 6 residues within 4Å: Chain A: H.912, C.913, A.970, G.971, R.988, D.1022 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain A: A.921, V.962, H.963, Y.964 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain A: Q.777, D.869, V.870, A.871 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain A: K.1238, V.1239, T.1240, E.1241 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain A: V.626, Q.627, L.629, P.757, G.758, D.760 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain A: A.719, R.723, D.765, K.768, A.769, E.773 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain A: Q.1010, Q.1014, E.1017 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain A: P.89, S.95, W.97, E.117, R.118, V.120 Ligand excluded by PLIP GOL.48: 9 residues within 4Å: Chain A: E.658, T.660, M.679, W.683, Q.684, R.992, E.1015, K.1019, R.1178 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain A: G.923, D.924, D.925 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain A: R.25, T.377, E.378, L.381, R.1006, R.1174 Ligand excluded by PLIP GOL.51: 4 residues within 4Å: Chain A: E.1183, T.1185, Q.1186, R.1231 Ligand excluded by PLIP GOL.52: 8 residues within 4Å: Chain A: H.285, G.288, R.579, I.1078, D.1079, D.1084, R.1089, I.1090 Ligand excluded by PLIP GOL.53: 3 residues within 4Å: Chain A: D.260, Y.261, E.274 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain A: Q.39, V.40, H.41, S.127 Ligand excluded by PLIP GOL.55: 2 residues within 4Å: Chain A: P.1025, N.1028 Ligand excluded by PLIP GOL.56: 5 residues within 4Å: Chain A: A.191, N.223, S.224, E.225, K.230 Ligand excluded by 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