SMTL ID : 6jt8.1

Crystal structure of 450-451_deletion mutant of FGAM Synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: V.440, T.587, E.588, E.589 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.588, A:E.589 EDO.2: 6 residues within 4Å: Chain A: K.335, G.389, R.485, V.666, T.667, N.1057 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.335, A:R.485, A:R.485, A:N.1057 Water bridges: A:K.335, A:P.336, A:P.336, A:P.336 EDO.3: 2 residues within 4Å: Chain A: T.789, R.790 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.790 Water bridges: A:R.790 EDO.4: 2 residues within 4Å: Chain A: R.942, Y.960 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.942, A:R.942 EDO.5: 5 residues within 4Å: Chain A: A.1044, R.1045, P.1046, R.1297 Ligands: SO4.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1297 Water bridges: A:R.1045, A:K.1047, A:R.1297 EDO.6: 1 residues within 4Å: Chain A: N.601 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.601 Water bridges: A:Q.602 EDO.7: 3 residues within 4Å: Chain A: R.818, H.819, R.883 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.818, A:R.883 EDO.8: 4 residues within 4Å: Chain A: Q.824, L.825, T.827, G.907 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.827, A:G.907 Water bridges: A:Q.824, A:Q.824 EDO.9: 2 residues within 4Å: Chain A: H.841, K.859 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.841, A:H.841 EDO.10: 3 residues within 4Å: Chain A: S.222, E.223, K.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.223, A:K.228 Water bridges: A:S.222, A:H.224, A:K.228 EDO.11: 3 residues within 4Å: Chain A: W.1278, P.1280, E.1281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1281 Water bridges: A:N.1282

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

ADP.12: 20 residues within 4Å: Chain A: V.341, F.343, T.394, G.395, Y.396, F.397, K.655, L.658, V.659, Q.674, P.682, A.684, D.685, E.724, N.728, D.890, S.892 Ligands: MG.48, MG.49, MG.50 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.394, A:T.394, A:G.395, A:Y.396, A:Y.396, A:Q.674, A:A.684, A:N.728, A:S.892 Water bridges: A:T.394, A:T.651, A:K.655, A:K.655, A:K.655, A:D.893, A:D.893, A:D.893 Salt bridges: A:K.655

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

SO4.13: 6 residues within 4Å: Chain A: H.224, T.303, H.304, N.305, H.306, S.784 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: H.1092, R.1132, P.1133, Q.1134, T.1135 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: G.1233, K.1234, V.1235 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: W.313, R.1165, R.1170 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: P.1046, K.1047, N.1090, H.1092 Ligands: EDO.5 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain A: S.20, A.21, F.22, N.1004, H.1167 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain A: N.1119, R.1121 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: Q.1182, Q.1189, G.1190, M.1191, V.1192 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: T.638, I.639 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: K.839, H.841, R.864 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: A.917, V.958, H.959 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain A: H.161, Q.162 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain A: N.1257, R.1259 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: R.5, G.6, S.7, H.160 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain A: P.364, E.365, R.366, W.791 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain A: Q.62, L.1117, F.1118, H.1120 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain A: H.224, E.302, G.510, A.511, K.782 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 6 residues within 4Å: Chain A: H.908, C.909, A.966, G.967, R.984, D.1018 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain A: R.23, T.375, E.376, R.1002, D.1169, R.1170 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain A: P.87, S.93, W.95, E.115, R.116 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain A: P.1155, G.1156, S.1157, E.1158, E.1256 Ligands: GOL.45 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain A: A.715, R.719, D.761, K.764, E.769 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain A: D.258, Y.259, E.272 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain A: N.842, G.919, D.920, D.921 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain A: V.622, Q.623, L.625, P.753, G.754, D.756 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain A: G.286, R.575, I.1074, D.1075, D.1080, R.1085, I.1086 Ligand excluded by PLIP GOL.39: 3 residues within 4Å: Chain A: K.644, E.982, W.990 Ligand excluded by PLIP GOL.40: 9 residues within 4Å: Chain A: E.654, T.656, M.675, W.679, Q.680, R.988, E.1011, K.1015, R.1174 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain A: E.272, A.275, P.294, H.296 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain A: Q.773, D.865, V.866, A.867 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain A: A.916, G.919, D.920, H.922, A.974, N.975, Q.977 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain A: K.1234, V.1235, T.1236, E.1237 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain A: H.1131, P.1155 Ligands: GOL.33 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain A: Q.37, V.38, H.39, A.124, S.125, T.126 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain A: G.751, H.752, P.753, K.788, R.790, E.799 Ligand excluded by PLIP

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

MG.48: 4 residues within 4Å: Chain A: D.685, N.728, D.890 Ligands: ADP.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.685, A:D.890, H2O.9, H2O.27 MG.49: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: E.724 Ligands: ADP.12 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.724, H2O.6, H2O.14, H2O.14, H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, N. et al., Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Sci Adv (2020)

Release Date

2020-03-04

Peptides

Phosphoribosylformylglycinamidine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoribosylformylglycinamidine synthase