SMTL ID : 4lgy.1

Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 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, D.894, S.896 Ligands: MG.2, MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.396, A:T.396, A:G.397, A:Y.398, A:Y.398, A:Q.678, A:A.688, A:N.732, A:S.896 Water bridges: A:T.396, A:K.659, A:K.659, A:K.659, A:D.897 Salt bridges: A:K.659

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

MG.2: 4 residues within 4Å: Chain A: D.689, N.732, D.894 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.689, A:D.894, H2O.40, H2O.40 MG.3: 2 residues within 4Å: Chain A: E.728 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.728, H2O.1, H2O.40, H2O.40, H2O.40 MG.4: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain A: F.1179 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: E.1241, T.1242 Ligands: GOL.27 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1242 MG.39: 4 residues within 4Å: Chain A: C.108, G.109, F.1122, N.1123 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain A: Q.737, H.823, A.885 No protein-ligand interaction detected (PLIP)

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

SO4.5: 5 residues within 4Å: Chain A: H.226, E.304, G.514, A.515, K.786 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: H.226, T.305, H.306, N.307, H.308, S.788 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: G.1237, K.1238, V.1239 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: P.366, E.367, R.368 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: P.1050, K.1051, H.1096 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: K.843, H.845, R.868 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: W.315, R.1169, R.1174 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: H.1096, R.1136, P.1137, Q.1138, T.1139 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: Q.1186, Q.1193, G.1194, M.1195, V.1196 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: A.921, V.962, H.963 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: Q.777, D.869, V.870, A.871 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: S.60, Q.64, L.1121, F.1122, H.1124 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: N.1123, R.1125 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: N.1261, R.1263 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain A: S.22, A.23, F.24, N.1008, Q.1010, H.1171 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain A: T.642, I.643 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: S.77, H.78, T.79 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: R.7, G.8, S.9, H.162 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: G.923, D.924, D.925 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.24: 4 residues within 4Å: Chain A: V.442, T.591, E.592, E.593 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.442, A:E.592 Hydrogen bonds: A:E.592, A:E.593 ACT.25: 2 residues within 4Å: Chain A: W.97, R.118 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.118, A:R.118, A:R.118, A:R.118, A:R.118 Salt bridges: A:R.118 ACT.26: 1 residues within 4Å: Chain A: T.257 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.257, A:T.257, A:T.257

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.27: 5 residues within 4Å: Chain A: K.1238, V.1239, T.1240, E.1241 Ligands: MG.38 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.1240, A:T.1240, A:E.1241 Water bridges: A:V.1239, A:E.1241 GOL.28: 6 residues within 4Å: Chain A: H.912, C.913, A.970, G.971, R.988, D.1022 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.971, A:G.971, A:R.988, A:D.1022 GOL.29: 4 residues within 4Å: Chain A: Q.1010, D.1013, Q.1014, E.1017 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.1009, A:D.1013, A:D.1013 GOL.30: 6 residues within 4Å: Chain A: T.93, I.94, S.95, P.96, M.146, R.482 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.94

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.31: 3 residues within 4Å: Chain A: Q.62, A.63, T.66 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: E.1183, V.1184, T.1185, G.1197 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain A: W.1282, H.1283 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: A.1112, E.1114, N.1153, F.1167 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain A: F.1134, N.1261, R.1263, V.1264 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain A: A.394, L.662, G.666 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanwar, A.S. et al., Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. Plos One (2013)

Release Date

2013-12-11

Peptides

Phosphoribosylformylglycinamidine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoribosylformylglycinamidine synthase