SMTL ID : 6jt9.1

Crystal Structure of D464A mutant of FGAM Synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: D.689, N.732, D.894 Ligands: ADP.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.689, A:D.894, H2O.8, H2O.9 MG.2: 2 residues within 4Å: Chain A: E.728 Ligands: ADP.16 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.728, H2O.3, H2O.10, H2O.12, H2O.15 MG.3: 1 residues within 4Å: Ligands: ADP.16 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: G.1237, K.1238, V.1239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.1239 Water bridges: A:V.1239 SO4.5: 5 residues within 4Å: Chain A: Q.1186, Q.1193, G.1194, M.1195, V.1196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.1186, A:G.1194, A:V.1196 Water bridges: A:S.1032 SO4.6: 4 residues within 4Å: Chain A: P.1050, K.1051, N.1094, H.1096 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.1051 Water bridges: A:H.1096 Salt bridges: A:K.1051, A:H.1096 SO4.7: 5 residues within 4Å: Chain A: H.1096, R.1136, P.1137, Q.1138, T.1139 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.1138 Water bridges: A:H.1096, A:H.1096, A:R.1136 Salt bridges: A:H.1096, A:R.1136 SO4.8: 2 residues within 4Å: Chain A: T.642, I.643 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.643 Water bridges: A:A.644 SO4.9: 3 residues within 4Å: Chain A: K.843, H.845, R.868 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.843, A:H.845 SO4.10: 2 residues within 4Å: Chain A: N.1261, R.1263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.1261 Water bridges: A:R.1263, A:R.1263, A:R.1263 Salt bridges: A:R.1263 SO4.11: 5 residues within 4Å: Chain A: A.921, V.962, H.963, Y.964 Ligands: GOL.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.964 Salt bridges: A:H.963 SO4.12: 6 residues within 4Å: Chain A: S.22, A.23, F.24, N.1008, Q.1010, H.1171 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.22, A:A.23, A:F.24, A:N.1008 Salt bridges: A:H.1171 SO4.13: 3 residues within 4Å: Chain A: P.366, E.367, R.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.367, A:R.368 Water bridges: A:Q.796 Salt bridges: A:R.368 SO4.14: 7 residues within 4Å: Chain A: T.305, H.306, N.307, H.308, P.309, K.419, S.788 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.307, A:H.308, A:S.788 Water bridges: A:K.419 Salt bridges: A:K.419 SO4.15: 2 residues within 4Å: Chain A: H.163, Q.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.164 Salt bridges: A:H.163

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

ADP.16: 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.1, MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.396, A:G.397, A:Y.398, A:Y.398, A:Q.678, A:A.688, A:D.689, A:E.728, A:E.728, A:N.732, A:D.894, A:S.896 Water bridges: A:T.655, A:K.659, A:K.659, A:K.659, A:K.659, A:D.897, A:D.897, A:E.906 Salt bridges: A:K.659

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: N.846, G.923, D.924, D.925 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.846, A:D.924, A:D.925 GOL.18: 4 residues within 4Å: Chain A: H.1135, P.1159, G.1160, E.1162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1160, A:E.1162 Water bridges: A:E.1131, A:H.1135 GOL.19: 4 residues within 4Å: Chain A: Q.777, D.869, V.870, A.871 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.777, A:V.870, A:A.871 GOL.20: 4 residues within 4Å: Chain A: W.315, R.1169, R.1174, F.1175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1169, A:R.1169, A:R.1174, A:F.1175 GOL.21: 5 residues within 4Å: Chain A: A.635, L.636, R.638, L.848, D.862 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.636, A:R.638, A:D.862 Water bridges: A:L.848, A:L.848 GOL.22: 4 residues within 4Å: Chain A: F.292, A.1068, H.1071, R.1072 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.1068, A:R.1072, A:R.1072 Water bridges: A:L.697 GOL.23: 3 residues within 4Å: Chain A: R.946, Y.964 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.946, A:R.946 GOL.24: 5 residues within 4Å: Chain A: G.755, H.756, P.757, R.794, E.803 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.794

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

CL.25: 3 residues within 4Å: Chain A: N.1028, V.1029, W.1282 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: H.78, T.79 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain A: R.1125 Ligand excluded by PLIP

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